Variant 1-156815970-AG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000368199.8(SH2D2A):c.123+35del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.56 ( 25694 hom., cov: 0)

Exomes 𝑓: 0.64 ( 304802 hom. )

Consequence

SH2D2A
ENST00000368199.8 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.239

Variant links:

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]

SH2D2A links:

NTRK1 (HGNC:8031): (neurotrophic receptor tyrosine kinase 1) This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, cognitive disability and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date. [provided by RefSeq, Jul 2008]

NTRK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-156815970-AG-A is Benign according to our data. Variant chr1-156815970-AG-A is described in ClinVar as [Benign]. Clinvar id is 1225268.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH2D2A	NM_003975.4 linkuse as main transcript	c.123+35del		intron_variant		ENST00000368199.8	NP_003966.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH2D2A	ENST00000368199.8 linkuse as main transcript	c.123+35del		intron_variant		1	NM_003975.4	ENSP00000357182	P2	Q9NP31-1

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85422

AN:

151364

Hom.:

25680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.337

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.582

Gnomad EAS

AF:

0.818

Gnomad SAS

AF:

0.646

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.642

Gnomad OTH

AF:

0.584

GnomAD3 exomes

AF:

0.631

AC:

154698

AN:

245012

Hom.:

49482

AF XY:

0.636

AC XY:

84228

AN XY:

132410

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.662

Gnomad ASJ exome

AF:

0.600

Gnomad EAS exome

AF:

0.812

Gnomad SAS exome

AF:

0.647

Gnomad FIN exome

AF:

0.629

Gnomad NFE exome

AF:

0.636

Gnomad OTH exome

AF:

0.628

GnomAD4 exome

AF:

0.644

AC:

936630

AN:

1455468

Hom.:

304802

Cov.:

AF XY:

0.645

AC XY:

466899

AN XY:

724024

show subpopulations

Gnomad4 AFR exome

AF:

0.314

Gnomad4 AMR exome

AF:

0.663

Gnomad4 ASJ exome

AF:

0.590

Gnomad4 EAS exome

AF:

0.817

Gnomad4 SAS exome

AF:

0.652

Gnomad4 FIN exome

AF:

0.632

Gnomad4 NFE exome

AF:

0.648

Gnomad4 OTH exome

AF:

0.635

GnomAD4 genome

AF:

0.564

AC:

85472

AN:

151486

Hom.:

25694

Cov.:

AF XY:

0.570

AC XY:

42132

AN XY:

73966

show subpopulations

Gnomad4 AFR

AF:

0.337

Gnomad4 AMR

AF:

0.646

Gnomad4 ASJ

AF:

0.582

Gnomad4 EAS

AF:

0.818

Gnomad4 SAS

AF:

0.647

Gnomad4 FIN

AF:

0.647

Gnomad4 NFE

AF:

0.642

Gnomad4 OTH

AF:

0.582

Alfa

AF:

0.537

Hom.:

3005

Bravo

AF:

0.558

Asia WGS

AF:

0.684

AC:

2379

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over