NM_001081573.3:c.73-998C>T

Variant names:

• chrX-154717327-G-A
• rs2664170
• NM_001081573.3:c.73-998C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001081573.3(GAB3):​c.73-998C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.63 (15535 hom., 19795 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: GAB3 NM_001081573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 40 publications found

Genes affected

GAB3 (HGNC:17515): (GRB2 associated binding protein 3) This gene is a member of the GRB2-associated binding protein gene family. These proteins are scaffolding/docking proteins that are involved in several growth factor and cytokine signaling pathways, and they contain a pleckstrin homology domain, and bind SHP2 tyrosine phosphatase and GRB2 adapter protein. The protein encoded by this gene facilitates macrophage differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAB3	NM_001081573.3	c.73-998C>T		intron_variant	Intron 1 of 9	ENST00000424127.3	NP_001075042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAB3	ENST00000424127.3	c.73-998C>T		intron_variant	Intron 1 of 9	1	NM_001081573.3	ENSP00000399588.2
GAB3	ENST00000369575.7	c.73-998C>T		intron_variant	Intron 1 of 9	1		ENSP00000358588.3
GAB3	ENST00000496390.5	n.93-998C>T		intron_variant	Intron 1 of 8	1
GAB3	ENST00000369568.8	c.73-998C>T		intron_variant	Intron 1 of 8	2		ENSP00000358581.4

Frequencies

GnomAD3 genomes AF: 0.626 AC: 68448 AN: 109335 Hom.: 15534 Cov.: 22

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.650

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.626 AC: 68466 AN: 109386 Hom.: 15535 Cov.: 22 AF XY: 0.625 AC XY: 19795 AN XY: 31692

African (AFR) AF: 0.509 AC: 15263 AN: 29974

American (AMR) AF: 0.612 AC: 6316 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 1728 AN: 2622

East Asian (EAS) AF: 0.800 AC: 2758 AN: 3447

South Asian (SAS) AF: 0.552 AC: 1383 AN: 2506

European-Finnish (FIN) AF: 0.703 AC: 3993 AN: 5677

Middle Eastern (MID) AF: 0.755 AC: 160 AN: 212

European-Non Finnish (NFE) AF: 0.675 AC: 35425 AN: 52472

Other (OTH) AF: 0.656 AC: 976 AN: 1487

Alfa AF: 0.661 Hom.: 77898

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.39
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2664170; hg19: chrX-153945602;