chr3-136341454-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_005862.3(STAG1):c.3544G>A(p.Val1182Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000103 in 1,458,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V1182V) has been classified as Likely benign.
Frequency
Consequence
NM_005862.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAG1 | NM_005862.3 | c.3544G>A | p.Val1182Met | missense_variant | 31/34 | ENST00000383202.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAG1 | ENST00000383202.7 | c.3544G>A | p.Val1182Met | missense_variant | 31/34 | 1 | NM_005862.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251090Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135716
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1458184Hom.: 0 Cov.: 29 AF XY: 0.00000827 AC XY: 6AN XY: 725714
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.3544G>A (p.V1182M) alteration is located in exon 31 (coding exon 30) of the STAG1 gene. This alteration results from a G to A substitution at nucleotide position 3544, causing the valine (V) at amino acid position 1182 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at