6-159069404-C-T

Variant names:

• chr6-159069404-C-T
• rs212388
• ENST00000645980.2:c.-271-4466G>A

Variant summary

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

The ENST00000645980.2(TAGAP):​c.-271-4466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,010 control chromosomes in the GnomAD database, including 20,323 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 0.50 (20323 hom., cov: 31)
• Consequence: TAGAP ENST00000645980.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 78 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 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.-271-4466G>A		intron	N/A	ENSP00000520449.1	A0AAQ5BID7
	ENSG00000285492	ENST00000642829.1		n.501-4466G>A		intron	N/A
	TAGAP-AS1	ENST00000643132.2		n.829-17149C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75918 AN: 151890 Hom.: 20322 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.499 AC: 75925 AN: 152010 Hom.: 20323 Cov.: 31 AF XY: 0.502 AC XY: 37305 AN XY: 74314

African (AFR) AF: 0.322 AC: 13331 AN: 41446

American (AMR) AF: 0.409 AC: 6247 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2059 AN: 5162

South Asian (SAS) AF: 0.578 AC: 2790 AN: 4824

European-Finnish (FIN) AF: 0.661 AC: 6992 AN: 10570

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40767 AN: 67946

Other (OTH) AF: 0.499 AC: 1054 AN: 2114

Alfa AF: 0.564 Hom.: 99813

Bravo AF: 0.469

Asia WGS AF: 0.494 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.78
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs212388; hg19: chr6-159490436;