2-85435769-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001394463.1(SH2D6):c.836G>A(p.Arg279Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000396 in 1,608,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001394463.1 missense
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 |
---|---|---|---|---|---|---|---|
SH2D6 | NM_001394463.1 | c.836G>A | p.Arg279Gln | missense_variant | 22/24 | ENST00000469800.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D6 | ENST00000469800.7 | c.836G>A | p.Arg279Gln | missense_variant | 22/24 | 3 | NM_001394463.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000181 AC: 43AN: 237020Hom.: 0 AF XY: 0.000178 AC XY: 23AN XY: 129072
GnomAD4 exome AF: 0.000422 AC: 614AN: 1456540Hom.: 0 Cov.: 32 AF XY: 0.000409 AC XY: 296AN XY: 724216
GnomAD4 genome AF: 0.000151 AC: 23AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at