rs879114

Positions:

• chr11-3622548-G-A

Variant summary

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

The ENST00000451043.7(TRPC2):​n.1125-94G>A variant causes a intron, non coding transcript 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 ENST00000451043.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPC2	ENST00000451043.7	n.1125-94G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.0938

Gnomad4 OTH exome AF: 0.125

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.227

Alfa AF: 0.187 Hom.: 5769

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879114; hg19: chr11-3643778;