chrX-124346690-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_002351.5(SH2D1A):c.48C>A(p.Gly16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000275 in 1,210,012 control chromosomes in the GnomAD database, including 7 homozygotes. There are 93 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G16G) has been classified as Likely benign.
Frequency
Consequence
NM_002351.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D1A | NM_002351.5 | c.48C>A | p.Gly16= | synonymous_variant | 1/4 | ENST00000371139.9 | |
SH2D1A | NM_001114937.3 | c.48C>A | p.Gly16= | synonymous_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D1A | ENST00000371139.9 | c.48C>A | p.Gly16= | synonymous_variant | 1/4 | 1 | NM_002351.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000436 AC: 49AN: 112347Hom.: 1 Cov.: 23 AF XY: 0.000521 AC XY: 18AN XY: 34529
GnomAD3 exomes AF: 0.00115 AC: 210AN: 183390Hom.: 3 AF XY: 0.000737 AC XY: 50AN XY: 67830
GnomAD4 exome AF: 0.000260 AC: 285AN: 1097613Hom.: 6 Cov.: 30 AF XY: 0.000207 AC XY: 75AN XY: 362977
GnomAD4 genome ? AF: 0.000427 AC: 48AN: 112399Hom.: 1 Cov.: 23 AF XY: 0.000520 AC XY: 18AN XY: 34591
ClinVar
Submissions by phenotype
X-linked lymphoproliferative disease due to SH2D1A deficiency Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 12, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at