chrX-124346690-C-T
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>T(p.Gly16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00315 in 1,210,010 control chromosomes in the GnomAD database, including 3 homozygotes. There are 1,222 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>T | p.Gly16= | synonymous_variant | 1/4 | ENST00000371139.9 | |
SH2D1A | NM_001114937.3 | c.48C>T | p.Gly16= | synonymous_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D1A | ENST00000371139.9 | c.48C>T | p.Gly16= | synonymous_variant | 1/4 | 1 | NM_002351.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00193 AC: 217AN: 112345Hom.: 0 Cov.: 23 AF XY: 0.00148 AC XY: 51AN XY: 34529
GnomAD3 exomes AF: 0.00198 AC: 363AN: 183390Hom.: 0 AF XY: 0.00201 AC XY: 136AN XY: 67830
GnomAD4 exome AF: 0.00327 AC: 3592AN: 1097613Hom.: 3 Cov.: 30 AF XY: 0.00323 AC XY: 1171AN XY: 362979
GnomAD4 genome ? AF: 0.00193 AC: 217AN: 112397Hom.: 0 Cov.: 23 AF XY: 0.00147 AC XY: 51AN XY: 34591
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 12, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 22, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2021 | This variant is associated with the following publications: (PMID: 9771704, 24616127) - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 24, 2017 | - - |
X-linked lymphoproliferative disease due to SH2D1A deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Mullegama-Klein-Martinez syndrome;C5393308:Holoprosencephaly 13, X-linked Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 08, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at