X-1633190-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001171038.2(ASMT):c.687C>A(p.Tyr229Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,682 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 33 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001171038.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASMT | NM_001171038.2 | c.687C>A | p.Tyr229Ter | stop_gained | 7/9 | ENST00000381241.9 | |
ASMT | NM_001416525.1 | c.603C>A | p.Tyr201Ter | stop_gained | 6/8 | ||
ASMT | NM_001171039.1 | c.563-3248C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.687C>A | p.Tyr229Ter | stop_gained | 7/9 | 1 | NM_001171038.2 | ||
ASMT | ENST00000381229.9 | c.603C>A | p.Tyr201Ter | stop_gained | 6/8 | 1 | P1 | ||
ASMT | ENST00000381233.8 | c.563-3248C>A | intron_variant | 1 | |||||
ASMT | ENST00000509780.6 | n.289-3052C>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74246
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251180Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135744
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461666Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727144
GnomAD4 genome AF: 0.000263 AC: 40AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74246
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 22, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at