1-156815073-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003975.4(SH2D2A):c.272C>A(p.Ala91Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,600,610 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D2A | NM_003975.4 | c.272C>A | p.Ala91Glu | missense_variant | 3/9 | ENST00000368199.8 | NP_003966.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D2A | ENST00000368199.8 | c.272C>A | p.Ala91Glu | missense_variant | 3/9 | 1 | NM_003975.4 | ENSP00000357182 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000418 AC: 10AN: 239254Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129738
GnomAD4 exome AF: 0.00000829 AC: 12AN: 1448238Hom.: 0 Cov.: 29 AF XY: 0.00000694 AC XY: 5AN XY: 720358
GnomAD4 genome AF: 0.000164 AC: 25AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.000174 AC XY: 13AN XY: 74518
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.272C>A (p.A91E) alteration is located in exon 3 (coding exon 3) of the SH2D2A gene. This alteration results from a C to A substitution at nucleotide position 272, causing the alanine (A) at amino acid position 91 to be replaced by a glutamic acid (E). 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