6-159061489-C-T

Variant names:

• chr6-159061489-C-T
• rs394581
• ENST00000642829.1:n.2890G>A

Variant summary

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

The ENST00000642829.1(ENSG00000285492):​n.2890G>A 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 0.69 in 152,006 control chromosomes in the GnomAD database, including 37,084 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 0.69 (37009 hom., cov: 30)
  • Exomes 𝑓: 0.74 (75 hom.)
• Consequence: ENSG00000285492 ENST00000642829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 33 publications found

Genes affected

ENSG00000285492 (HGNC:):

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]

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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
ENSG00000285492	ENST00000642829.1	n.2890G>A		non_coding_transcript_exon_variant	Exon 5 of 5
TAGAP	ENST00000645980.2	c.-101+3279G>A		intron_variant	Intron 2 of 6			ENSP00000520449.1
TAGAP-AS1	ENST00000606470.2	n.541-3390C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104679 AN: 151632 Hom.: 36981 Cov.: 30

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.686

GnomAD4 exome AF: 0.742 AC: 190 AN: 256 Hom.: 75 Cov.: 0 AF XY: 0.723 AC XY: 149 AN XY: 206

African (AFR) AF: 0.375 AC: 3 AN: 8

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 4 AN: 6

East Asian (EAS) AF: 1.00 AC: 10 AN: 10

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.764 AC: 159 AN: 208

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.690 AC: 104751 AN: 151750 Hom.: 37009 Cov.: 30 AF XY: 0.700 AC XY: 51935 AN XY: 74142

African (AFR) AF: 0.554 AC: 22870 AN: 41294

American (AMR) AF: 0.758 AC: 11569 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3468

East Asian (EAS) AF: 0.920 AC: 4730 AN: 5142

South Asian (SAS) AF: 0.828 AC: 3983 AN: 4810

European-Finnish (FIN) AF: 0.810 AC: 8522 AN: 10524

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48445 AN: 67944

Other (OTH) AF: 0.690 AC: 1451 AN: 2102

Alfa AF: 0.703 Hom.: 56607

Bravo AF: 0.679

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs394581; hg19: chr6-159482521; COSMIC: COSV71541262;