rs10793294

chr11-78285357-C-Achr11-78285357-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080491.3(GAB2):c.76-4456G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,120 control chromosomes in the GnomAD database, including 31,623 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (31623 hom., cov: 33)
• Consequence: GAB2 NM_080491.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

GAB2 (HGNC:14458): (GRB2 associated binding protein 2) This gene is a member of the GRB2-associated binding protein (GAB) gene family. These proteins contain pleckstrin homology (PH) domain, and bind SHP2 tyrosine phosphatase and GRB2 adapter protein. They act as adapters for transmitting various signals in response to stimuli through cytokine and growth factor receptors, and T- and B-cell antigen receptors. The protein encoded by this gene is the principal activator of phosphatidylinositol-3 kinase in response to activation of the high affinity IgE receptor. Two alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAB2	NM_080491.3	c.76-4456G>T		intron_variant		ENST00000361507.5
GAB2	NM_012296.4	c.-39-4456G>T		intron_variant
GAB2	XM_024448782.2	c.22-4456G>T		intron_variant
GAB2	XM_047427935.1	c.-39-4456G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAB2	ENST00000361507.5	c.76-4456G>T		intron_variant		1	NM_080491.3	P1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94015 AN: 152002 Hom.: 31628 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.633

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.618 AC: 94030 AN: 152120 Hom.: 31623 Cov.: 33 AF XY: 0.607 AC XY: 45135 AN XY: 74376

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.630

Alfa AF: 0.749 Hom.: 69383

Bravo AF: 0.610

Asia WGS AF: 0.322 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	10
Dann	Benign	0.85

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

Other links and lift over

dbSNP: rs10793294; hg19: chr11-77996403;