1-156807267-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_003975.4(SH2D2A):āc.1081G>Cā(p.Ala361Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Likely benign (ā ).
Frequency
Genomes: š 0.00013 ( 0 hom., cov: 0)
Exomes š: 0.0024 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SH2D2A
NM_003975.4 missense
NM_003975.4 missense
Scores
19
Clinical Significance
Conservation
PhyloP100: -0.169
Genes affected
SH2D2A (HGNC:10821): (SH2 domain containing 2A) This gene encodes an adaptor protein thought to function in T-cell signal transduction. A related protein in mouse is responsible for the activation of lymphocyte-specific protein-tyrosine kinase and functions in downstream signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.048122466).
BP6
Variant 1-156807267-C-G is Benign according to our data. Variant chr1-156807267-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2471514.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D2A | NM_003975.4 | c.1081G>C | p.Ala361Pro | missense_variant | 8/9 | ENST00000368199.8 | NP_003966.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D2A | ENST00000368199.8 | c.1081G>C | p.Ala361Pro | missense_variant | 8/9 | 1 | NM_003975.4 | ENSP00000357182 | P2 | |
SH2D2A | ENST00000392306.2 | c.1111G>C | p.Ala371Pro | missense_variant | 8/9 | 1 | ENSP00000376123 | |||
SH2D2A | ENST00000368198.7 | c.1027G>C | p.Ala343Pro | missense_variant | 8/9 | 1 | ENSP00000357181 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7AN: 53190Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 genomes
AF:
AC:
7
AN:
53190
Hom.:
Cov.:
0
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000133 AC: 19AN: 142480Hom.: 0 AF XY: 0.000125 AC XY: 10AN XY: 80304
GnomAD3 exomes
AF:
AC:
19
AN:
142480
Hom.:
AF XY:
AC XY:
10
AN XY:
80304
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00239 AC: 481AN: 200870Hom.: 0 Cov.: 0 AF XY: 0.00243 AC XY: 268AN XY: 110426
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
481
AN:
200870
Hom.:
Cov.:
0
AF XY:
AC XY:
268
AN XY:
110426
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000132 AC: 7AN: 53220Hom.: 0 Cov.: 0 AF XY: 0.000118 AC XY: 3AN XY: 25496
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
7
AN:
53220
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
25496
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;N;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0, 0.0010
.;B;B
Vest4
MutPred
0.16
.;Gain of glycosylation at A361 (P = 0.0021);.;
MVP
MPC
0.33
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at