6-159085568-C-T

Variant names:

• chr6-159085568-C-T
• rs2451258
• ENST00000645980.2:c.-272+10161G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645980.2(TAGAP):​c.-272+10161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 151,840 control chromosomes in the GnomAD database, including 43,890 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 0.75 (43890 hom., cov: 29)
• Consequence: TAGAP ENST00000645980.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 59 publications found

Genes affected

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]

LOC112267968 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645980.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAGAP	ENST00000645980.2		c.-272+10161G>A		intron	N/A	ENSP00000520449.1	A0AAQ5BID7
	ENSG00000285492	ENST00000642829.1		n.500+10161G>A		intron	N/A
	TAGAP-AS1	ENST00000643132.2		n.829-985C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 113972 AN: 151722 Hom.: 43828 Cov.: 29

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.751 AC: 114095 AN: 151840 Hom.: 43890 Cov.: 29 AF XY: 0.758 AC XY: 56251 AN XY: 74166

African (AFR) AF: 0.894 AC: 37025 AN: 41428

American (AMR) AF: 0.794 AC: 12119 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4805 AN: 5152

South Asian (SAS) AF: 0.783 AC: 3764 AN: 4806

European-Finnish (FIN) AF: 0.733 AC: 7695 AN: 10492

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44111 AN: 67922

Other (OTH) AF: 0.741 AC: 1560 AN: 2106

Alfa AF: 0.696 Hom.: 102780

Bravo AF: 0.763

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs2451258; hg19: chr6-159506600;