X-1633209-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001171038.2(ASMT):c.706G>A(p.Val236Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001171038.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASMT | NM_001171038.2 | c.706G>A | p.Val236Ile | missense_variant | 7/9 | ENST00000381241.9 | |
ASMT | NM_001416525.1 | c.622G>A | p.Val208Ile | missense_variant | 6/8 | ||
ASMT | NM_001171039.1 | c.563-3229G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.706G>A | p.Val236Ile | missense_variant | 7/9 | 1 | NM_001171038.2 | ||
ASMT | ENST00000381229.9 | c.622G>A | p.Val208Ile | missense_variant | 6/8 | 1 | P1 | ||
ASMT | ENST00000381233.8 | c.563-3229G>A | intron_variant | 1 | |||||
ASMT | ENST00000509780.6 | n.289-3033G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74264
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251178Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135744
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461652Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 727138
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Jul 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at