6-159063744-T-C

Variant names:

• chr6-159063744-T-C
• rs169858
• XM_047419645.1:c.495-37A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047419645.1(LOC112267968):​c.495-37A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,598 control chromosomes in the GnomAD database, including 44,530 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 0.76 (44389 hom., cov: 31)
  • Exomes 𝑓: 0.74 (141 hom.)
• Consequence: LOC112267968 XM_047419645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

LOC112267968 (HGNC:):

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

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267968	XM_047419645.1	c.495-37A>G		intron_variant	Intron 4 of 4		XP_047275601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAGAP-AS1	ENST00000606470.1	n.541-1135T>C		intron_variant	Intron 2 of 2	5
ENSG00000285492	ENST00000642829.1	n.672-37A>G		intron_variant	Intron 4 of 4
TAGAP-AS1	ENST00000643132.2	n.828+21436T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115585 AN: 151986 Hom.: 44346 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.744 AC: 366 AN: 492 Hom.: 141 Cov.: 0 AF XY: 0.750 AC XY: 246 AN XY: 328

Gnomad4 AFR exome AF: 0.875

Gnomad4 AMR exome AF: 0.875

Gnomad4 ASJ exome AF: 0.625

Gnomad4 EAS exome AF: 0.800

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.756

Gnomad4 NFE exome AF: 0.723

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.761 AC: 115679 AN: 152106 Hom.: 44389 Cov.: 31 AF XY: 0.769 AC XY: 57175 AN XY: 74368

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.757

Alfa AF: 0.717 Hom.: 80032

Bravo AF: 0.762

Asia WGS AF: 0.879 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169858; hg19: chr6-159484776;