chrX-1633124-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001171038.2(ASMT):c.647-26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,613,766 control chromosomes in the GnomAD database, including 1 homozygotes. There are 111 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001171038.2 intron
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.647-26G>A | intron_variant | ENST00000381241.9 | |||
ASMT | NM_001171039.1 | c.562+3185G>A | intron_variant | ||||
ASMT | NM_001416525.1 | c.563-26G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASMT | ENST00000381241.9 | c.647-26G>A | intron_variant | 1 | NM_001171038.2 | ||||
ASMT | ENST00000381229.9 | c.563-26G>A | intron_variant | 1 | P1 | ||||
ASMT | ENST00000381233.8 | c.562+3185G>A | intron_variant | 1 | |||||
ASMT | ENST00000509780.6 | n.289-3118G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000645 AC: 98AN: 152052Hom.: 1 Cov.: 32 AF XY: 0.000673 AC XY: 50AN XY: 74266
GnomAD3 exomes AF: 0.000243 AC: 61AN: 250994Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135622
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461596Hom.: 0 Cov.: 34 AF XY: 0.0000825 AC XY: 60AN XY: 727096
GnomAD4 genome AF: 0.000657 AC: 100AN: 152170Hom.: 1 Cov.: 32 AF XY: 0.000686 AC XY: 51AN XY: 74394
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at