rs212402

Variant names:

• chr6-159051263-G-A
• rs212402
• ENST00000606470.1:n.540+8955G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-159051263-G-A
• chr6-159051263-G-C
• chr6-159051263-G-T

Variant summary

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

The ENST00000645980.1(ENSG00000226032):​n.267-6343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000226032 ENST00000645980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

Genes affected

TAGAP-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAGAP-AS1	ENST00000606470.1	n.540+8955G>A		intron_variant	Intron 2 of 2	5
TAGAP-AS1	ENST00000643132.2	n.828+8955G>A		intron_variant	Intron 4 of 4
ENSG00000226032	ENST00000645980.1	n.267-6343C>T		intron_variant	Intron 2 of 6			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;