6-159061489-C-T

Position:

• chr6-159061489-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285492 (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=-0.89).
• 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/exons	MANE	Protein	UniProt
		n.159061489C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285492	ENST00000642829.1	n.2890G>A		non_coding_transcript_exon_variant	5/5
TAGAP-AS1	ENST00000606470.1	n.541-3390C>T		intron_variant		5
TAGAP-AS1	ENST00000643132.2	n.828+19181C>T		intron_variant

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

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.764

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.690

Alfa AF: 0.713 Hom.: 6771

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

Splicing

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

Publications

LitVar

Other links and lift over

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