chr6-159051263-G-A

Position:

• chr6-159051263-G-A

Variant summary

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

The variant allele was found at a frequency of 0.663 in 149,898 control chromosomes in the GnomAD database, including 33,445 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 0.66 (33445 hom., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

Genes affected

(HGNC:):

ENSG00000226032 (HGNC:15669): (T cell activation RhoGTPase activating protein) This gene encodes a member of the Rho GTPase-activator protein superfamily. The encoded protein may function as a Rho GTPase-activating protein. Alterations in this gene may be associated with several diseases, including rheumatoid arthritis, celiac disease, and multiple sclerosis. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159051263G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAGAP-AS1	ENST00000606470.1	n.540+8955G>A		intron_variant		5
TAGAP-AS1	ENST00000643132.2	n.828+8955G>A		intron_variant
ENSG00000226032	ENST00000645980.1	n.267-6343C>T		intron_variant				ENSP00000520449.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 99353 AN: 149788 Hom.: 33429 Cov.: 24

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.663 AC: 99400 AN: 149898 Hom.: 33445 Cov.: 24 AF XY: 0.672 AC XY: 49076 AN XY: 73030

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.682

Alfa AF: 0.666 Hom.: 18352

Bravo AF: 0.663

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs212402; hg19: chr6-159472295; COSMIC: COSV74190184;