6-159048542-A-G

Variant names:

• chr6-159048542-A-G
• rs182429
• ENST00000685651.1:n.1504A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

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

TAGAP (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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGAP-AS1	ENST00000685651.1		n.1504A>G		non_coding_transcript_exon	Exon 4 of 4
	TAGAP-AS1	ENST00000819080.1		n.1795A>G		non_coding_transcript_exon	Exon 5 of 5
	TAGAP-AS1	ENST00000819081.1		n.1561A>G		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.324 AC: 13419 AN: 41466

American (AMR) AF: 0.460 AC: 7027 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2046 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2148 AN: 5166

South Asian (SAS) AF: 0.615 AC: 2966 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6073 AN: 10550

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39537 AN: 67936

Other (OTH) AF: 0.506 AC: 1070 AN: 2114

Alfa AF: 0.546 Hom.: 29430

Bravo AF: 0.469

Asia WGS AF: 0.547 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.67
PhyloP100		0.17

Splicing

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

Other links and lift over

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