rs1107943

Variant names:

• chr6-159077235-T-C
• rs1107943
• XM_047419645.1:c.324-12297A>G

Variant summary

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

The XM_047419645.1(LOC112267968):​c.324-12297A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 152,282 control chromosomes in the GnomAD database, including 267 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 0.050 (267 hom., cov: 32)
• Consequence: LOC112267968 XM_047419645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267968	XM_047419645.1	c.324-12297A>G		intron_variant	Intron 3 of 4		XP_047275601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285492	ENST00000642829.1	n.501-12297A>G		intron_variant	Intron 3 of 4
TAGAP-AS1	ENST00000643132.2	n.829-9318T>C		intron_variant	Intron 4 of 4
ENSG00000226032	ENST00000645980.1	n.96-12297A>G		intron_variant	Intron 1 of 6			ENSP00000520449.1

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7668 AN: 152164 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0503 AC: 7665 AN: 152282 Hom.: 267 Cov.: 32 AF XY: 0.0499 AC XY: 3714 AN XY: 74456

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.0743

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0646 Hom.: 73

Bravo AF: 0.0440

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107943; hg19: chr6-159498267;