rs947992

Variant names:

• chr11-101614310-T-A
• rs947992
• ENST00000526713.1:n.266-109512A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-101614310-T-A
• chr11-101614310-T-C

Variant summary

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

The ENST00000526713.1(TRPC6):​n.266-109512A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,232 control chromosomes in the GnomAD database, including 51,554 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 0.82 (51554 hom., cov: 33)
• Consequence: TRPC6 ENST00000526713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

TRPC6 (HGNC:12338): (transient receptor potential cation channel subfamily C member 6) The protein encoded by this gene forms a receptor-activated calcium channel in the cell membrane. The channel is activated by diacylglycerol and is thought to be under the control of a phosphatidylinositol second messenger system. Activation of this channel occurs independently of protein kinase C and is not triggered by low levels of intracellular calcium. Defects in this gene are a cause of focal segmental glomerulosclerosis 2 (FSGS2). [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
TRPC6	ENST00000526713.1	n.266-109512A>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124269 AN: 152114 Hom.: 51482 Cov.: 33

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.817 AC: 124400 AN: 152232 Hom.: 51554 Cov.: 33 AF XY: 0.817 AC XY: 60825 AN XY: 74410

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.797

Alfa AF: 0.701 Hom.: 2050

Bravo AF: 0.830

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947992; hg19: chr11-101485041;