chr11-101722330-C-T

Position:

• chr11-101722330-C-T

Variant summary

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

The variant allele was found at a frequency of 0.283 in 152,088 control chromosomes in the GnomAD database, including 8,025 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 0.28 (8025 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

(HGNC:):

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 = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101722330C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPC6	ENST00000526713.1	n.265+149968G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42960 AN: 151970 Hom.: 8010 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.283 AC: 42982 AN: 152088 Hom.: 8025 Cov.: 32 AF XY: 0.286 AC XY: 21258 AN XY: 74326

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.314

Alfa AF: 0.326 Hom.: 7511

Bravo AF: 0.284

Asia WGS AF: 0.558 AC: 1937 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.99
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895184; hg19: chr11-101593061;