X-1615250-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001171038.2(ASMT):c.51C>A(p.Asn17Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,595,758 control chromosomes in the GnomAD database, including 126 homozygotes. There are 3,268 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_001171038.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASMT | NM_001171038.2 | c.51C>A | p.Asn17Lys | missense_variant | 1/9 | ENST00000381241.9 | |
ASMT | NM_001416525.1 | c.51C>A | p.Asn17Lys | missense_variant | 1/8 | ||
ASMT | NM_001171039.1 | c.51C>A | p.Asn17Lys | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.51C>A | p.Asn17Lys | missense_variant | 1/9 | 1 | NM_001171038.2 | ||
ASMT | ENST00000381229.9 | c.51C>A | p.Asn17Lys | missense_variant | 1/8 | 1 | P1 | ||
ASMT | ENST00000381233.8 | c.51C>A | p.Asn17Lys | missense_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00295 AC: 449AN: 152066Hom.: 8 Cov.: 31 AF XY: 0.00362 AC XY: 269AN XY: 74264
GnomAD3 exomes AF: 0.00680 AC: 1492AN: 219496Hom.: 37 AF XY: 0.00843 AC XY: 995AN XY: 118066
GnomAD4 exome AF: 0.00312 AC: 4501AN: 1443574Hom.: 118 Cov.: 32 AF XY: 0.00418 AC XY: 2995AN XY: 716094
GnomAD4 genome AF: 0.00298 AC: 453AN: 152184Hom.: 8 Cov.: 31 AF XY: 0.00367 AC XY: 273AN XY: 74392
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 13, 2023 | - - |
ASMT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 20, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at