2-85436538-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394463.1(SH2D6):c.964G>A(p.Gly322Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,613,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394463.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D6 | NM_001394463.1 | c.964G>A | p.Gly322Ser | missense_variant | 23/24 | ENST00000469800.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D6 | ENST00000469800.7 | c.964G>A | p.Gly322Ser | missense_variant | 23/24 | 3 | NM_001394463.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250878Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135736
GnomAD4 exome AF: 0.000101 AC: 147AN: 1461330Hom.: 0 Cov.: 31 AF XY: 0.0000922 AC XY: 67AN XY: 727004
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 28, 2022 | The c.484G>A (p.G162S) alteration is located in exon 4 (coding exon 4) of the SH2D6 gene. This alteration results from a G to A substitution at nucleotide position 484, causing the glycine (G) at amino acid position 162 to be replaced by a serine (S). 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