1-156809222-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003975.4(SH2D2A):c.983G>A(p.Arg328Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,612,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.983G>A | p.Arg328Lys | 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.983G>A | p.Arg328Lys | missense_variant | 7/9 | 1 | NM_003975.4 | ENSP00000357182 | P2 | |
SH2D2A | ENST00000392306.2 | c.1013G>A | p.Arg338Lys | missense_variant | 7/9 | 1 | ENSP00000376123 | |||
SH2D2A | ENST00000368198.7 | c.929G>A | p.Arg310Lys | missense_variant | 7/9 | 1 | ENSP00000357181 | A2 | ||
SH2D2A | ENST00000468744.5 | n.680G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000561 AC: 14AN: 249744Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134942
GnomAD4 exome AF: 0.000162 AC: 236AN: 1460354Hom.: 0 Cov.: 33 AF XY: 0.000160 AC XY: 116AN XY: 726330
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.1013G>A (p.R338K) alteration is located in exon 7 (coding exon 7) of the SH2D2A gene. This alteration results from a G to A substitution at nucleotide position 1013, causing the arginine (R) at amino acid position 338 to be replaced by a lysine (K). 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