11-3622548-G-A

Variant names:

• chr11-3622548-G-A
• rs879114
• ENST00000451043.8:n.1125-94G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451043.8(TRPC2):​n.1125-94G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,470 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3004 hom., cov: 31)
  • Exomes 𝑓: 0.13 (4 hom.)
• Consequence: TRPC2 ENST00000451043.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 3 publications found

Genes affected

TRPC2 (HGNC:12334): (transient receptor potential cation channel subfamily C member 2 (pseudogene)) Predicted to enable several functions, including calmodulin binding activity; diacylglycerol binding activity; and inositol 1,4,5 trisphosphate binding activity. Predicted to act upstream of or within several processes, including inter-male aggressive behavior; mating behavior; and territorial aggressive behavior. Predicted to be located in several cellular components, including Golgi membrane; dendrite membrane; and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 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
TRPC2	ENST00000451043.8	n.1125-94G>A		intron_variant	Intron 3 of 11

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29380 AN: 151872 Hom.: 3000 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.225

GnomAD4 exome AF: 0.126 AC: 60 AN: 478 Hom.: 4 AF XY: 0.0903 AC XY: 26 AN XY: 288

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.128 AC: 56 AN: 436

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0938 AC: 3 AN: 32

Other (OTH) AF: 0.125 AC: 1 AN: 8

GnomAD4 genome AF: 0.193 AC: 29406 AN: 151992 Hom.: 3004 Cov.: 31 AF XY: 0.194 AC XY: 14383 AN XY: 74290

African (AFR) AF: 0.243 AC: 10067 AN: 41426

American (AMR) AF: 0.178 AC: 2723 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3466

East Asian (EAS) AF: 0.161 AC: 830 AN: 5170

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4800

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10580

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11668 AN: 67966

Other (OTH) AF: 0.227 AC: 478 AN: 2106

Alfa AF: 0.187 Hom.: 12488

Bravo AF: 0.199

Asia WGS AF: 0.208 AC: 723 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	3.8
DANN	Benign	0.71
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs879114; hg19: chr11-3643778;