MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000555427
Querying Taster for transcript #2: ENST00000556922
Querying Taster for transcript #3: ENST00000639847
Querying Taster for transcript #4: ENST00000555147
MT speed 0.77 s - this script 3.125652 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000555427	MC1R	Benign	2\|198	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000639847	MC1R	Benign	33\|67	3utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000555147(MANE Select)	MC1R	Benign	33\|67	3utr	No	Single base exchange	N/A	Homozygous in gnomAD

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

16:89920224G>A_1_ENST00000555427

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:89920224G>A (GRCh38)

Gene symbol

MC1R

Gene constraints

LOEUF: 1.92, LOF (oe): 1.51, misssense (oe): 1.26, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000555427.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.950+16G>A
g.8106G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3212368
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	944	10849	11793

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0
	1.352	0.004
(flanking)	-0.814	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

16

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

16

Strand

1

Original gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACGCGGCTTTAAGTGTGCTGGGC

Altered gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACACGGCTTTAAGTGTGCTGGGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAVQGSQRRL LGSLNSTPTA IPQLGLAANQ TGARCLEVSI SDGLFLSLGL VSLVENALVV
ATIAKNRNLH SPMYCFICCL ALSDLLVSGS NVLETAVILL LEAGALVARA AVLQQLDNVI
DVITCSSMLS SLCFLGAIAV DRYISIFYAL RYHSIVTLPR ARRAVAAIWV ASVVFSTLFI
AYYDHVAVLL CLVVFFLAML VLMAVLYVHM LARACQHAQG IARLHKRQRP VHQGFGLKGA
VTLTILLGIF FLCWGPFFLH LTLIVLCPEH PTCGCIFKNF NLFLALIICN AIIDPLIYAF
HSQELRRTLK EVLTCSCSQD RALVSWDVKS LGGSVCQELL PQQPQEKGLC DQKASSTALQ
RLLQKEVKSL PQAKGPGLQE PP*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

2304 / 2304

Last intron/exon boundary

3253

Theoretical NMD boundary in CDS

899

Length of CDS

1149

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

8106

Chromosomal position

89920224

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

16:89920224G>A_3_ENST00000639847

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 33|67 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:89920224G>A (GRCh38)

Gene symbol

MC1R

Gene constraints

LOEUF: 1.93, LOF (oe): 1.54, misssense (oe): 1.26, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000639847.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1840G>A
g.8106G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3212368
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	944	10849	11793

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0
	1.352	0.004
(flanking)	-0.814	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

16

Strand

1

Original gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACGCGGCTTTAAGTGTGCTGGGC

Altered gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACACGGCTTTAAGTGTGCTGGGC

Original cDNA sequence snippet

TCCTGGTGAGCGCGGTGCACGCGGCTTTAAGTGTGCTGGGC

Altered cDNA sequence snippet

TCCTGGTGAGCGCGGTGCACACGGCTTTAAGTGTGCTGGGC

Wildtype AA sequence

MAVQGSQRRL LGSLNSTPTA IPQLGLAANQ TGARCLEVSI SDGLFLSLGL VSLVENALVV
ATIAKNRNLH SPMYCFICCL ALSDLLVSGS NVLETAVILL LEAGALVARA AVLQQLDNVI
DVITCSSMLS SLCFLGAIAV DRYISIFYAL RYHSIVTLPR ARRAVAAIWV ASVVFSTLFI
AYYDHVAVLL CLVVFFLAML VLMAVLYVHM LARACQHAQG IARLHKRQRP VHQGFGLKGA
VTLTILLGIF FLCWGPFFLH LTLIVLCPEH PTCGCIFKNF NLFLALIICN AIIDPLIYAF
HSQELRRTLK EVLTCSW*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

875 / 875

Last intron/exon boundary

466

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

954

Coding sequence (CDS) position

N/A

cDNA position

1840

gDNA position

8106

Chromosomal position

89920224

Speed

0.39 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

16:89920224G>A_4_ENST00000555147

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 33|67 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:89920224G>A (GRCh38)

Gene symbol

MC1R

Gene constraints

LOEUF: 1.93, LOF (oe): 1.54, misssense (oe): 1.26, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000555147.2

Genbank transcript ID

NM_002386 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1363G>A
g.8106G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3212368
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	944	10849	11793

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0
	1.352	0.004
(flanking)	-0.814	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

16

Strand

1

Original gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACGCGGCTTTAAGTGTGCTGGGC

Altered gDNA sequence snippet

TCCTGGTGAGCGCGGTGCACACGGCTTTAAGTGTGCTGGGC

Original cDNA sequence snippet

TCCTGGTGAGCGCGGTGCACGCGGCTTTAAGTGTGCTGGGC

Altered cDNA sequence snippet

TCCTGGTGAGCGCGGTGCACACGGCTTTAAGTGTGCTGGGC

Wildtype AA sequence

MAVQGSQRRL LGSLNSTPTA IPQLGLAANQ TGARCLEVSI SDGLFLSLGL VSLVENALVV
ATIAKNRNLH SPMYCFICCL ALSDLLVSGS NVLETAVILL LEAGALVARA AVLQQLDNVI
DVITCSSMLS SLCFLGAIAV DRYISIFYAL RYHSIVTLPR ARRAVAAIWV ASVVFSTLFI
AYYDHVAVLL CLVVFFLAML VLMAVLYVHM LARACQHAQG IARLHKRQRP VHQGFGLKGA
VTLTILLGIF FLCWGPFFLH LTLIVLCPEH PTCGCIFKNF NLFLALIICN AIIDPLIYAF
HSQELRRTLK EVLTCSW*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

398 / 398

Last intron/exon boundary

0

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

954

Coding sequence (CDS) position

N/A

cDNA position

1363

gDNA position

8106

Chromosomal position

89920224

Speed

0.35 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

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