1-156809429-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003975.4(SH2D2A):c.776T>A(p.Val259Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,613,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003975.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D2A | NM_003975.4 | c.776T>A | p.Val259Asp | missense_variant | 7/9 | ENST00000368199.8 | NP_003966.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D2A | ENST00000368199.8 | c.776T>A | p.Val259Asp | missense_variant | 7/9 | 1 | NM_003975.4 | ENSP00000357182 | P2 | |
SH2D2A | ENST00000392306.2 | c.806T>A | p.Val269Asp | missense_variant | 7/9 | 1 | ENSP00000376123 | |||
SH2D2A | ENST00000368198.7 | c.722T>A | p.Val241Asp | missense_variant | 7/9 | 1 | ENSP00000357181 | A2 | ||
SH2D2A | ENST00000468744.5 | n.473T>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151948Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250380Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135302
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461102Hom.: 0 Cov.: 33 AF XY: 0.0000812 AC XY: 59AN XY: 726776
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151948Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.806T>A (p.V269D) alteration is located in exon 7 (coding exon 7) of the SH2D2A gene. This alteration results from a T to A substitution at nucleotide position 806, causing the valine (V) at amino acid position 269 to be replaced by an aspartic acid (D). 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