rs182429

Positions:

• chr6-159048542-A-G
• chr6-159048542-A-T

Variant summary

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

The ENST00000685651.1(TAGAP-AS1):​n.1504A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,988 control chromosomes in the GnomAD database, including 19,579 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 0.49 (19579 hom., cov: 31)
• Consequence: TAGAP-AS1 ENST00000685651.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

TAGAP-AS1 (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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159048542A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAGAP-AS1	ENST00000685651.1	n.1504A>G		non_coding_transcript_exon_variant	4/4
TAGAP-AS1	ENST00000606470.1	n.540+6234A>G		intron_variant		5
TAGAP-AS1	ENST00000643132.2	n.828+6234A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74968 AN: 151870 Hom.: 19584 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.493 AC: 74981 AN: 151988 Hom.: 19579 Cov.: 31 AF XY: 0.496 AC XY: 36873 AN XY: 74288

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.506

Alfa AF: 0.559 Hom.: 23142

Bravo AF: 0.469

Asia WGS AF: 0.547 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs182429; hg19: chr6-159469574; COSMIC: COSV57850972;