X-1636511-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001171038.2(ASMT):c.861C>T(p.Asp287=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0928 in 1,613,588 control chromosomes in the GnomAD database, including 8,241 homozygotes. There are 73,489 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. D287D) has been classified as Benign.
Frequency
Consequence
NM_001171038.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASMT | NM_001171038.2 | c.861C>T | p.Asp287= | synonymous_variant | 8/9 | ENST00000381241.9 | |
ASMT | NM_001416525.1 | c.777C>T | p.Asp259= | synonymous_variant | 7/8 | ||
ASMT | NM_001171039.1 | c.636C>T | p.Asp212= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.861C>T | p.Asp287= | synonymous_variant | 8/9 | 1 | NM_001171038.2 |
Frequencies
GnomAD3 genomes AF: 0.104 AC: 15870AN: 151944Hom.: 974 Cov.: 31 AF XY: 0.105 AC XY: 7810AN XY: 74210
GnomAD3 exomes AF: 0.106 AC: 26690AN: 251166Hom.: 1928 AF XY: 0.0999 AC XY: 13556AN XY: 135728
GnomAD4 exome AF: 0.0916 AC: 133892AN: 1461526Hom.: 7269 Cov.: 32 AF XY: 0.0903 AC XY: 65661AN XY: 727040
GnomAD4 genome AF: 0.104 AC: 15880AN: 152062Hom.: 972 Cov.: 31 AF XY: 0.105 AC XY: 7828AN XY: 74338
ClinVar
Submissions by phenotype
ASMT-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2021 | This variant is classified as 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