rs2009568

Positions:

• chr11-3623585-G-C
• chr11-3623585-G-T

Variant summary

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

The ENST00000451043.7(TRPC2):​n.1299+769G>C 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 0.986 in 152,286 control chromosomes in the GnomAD database, including 74,031 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 0.99 (74031 hom., cov: 31)
• Consequence: TRPC2 ENST00000451043.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 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.1299+769G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.986 AC: 149992 AN: 152168 Hom.: 73970 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.986 AC: 150113 AN: 152286 Hom.: 74031 Cov.: 31 AF XY: 0.987 AC XY: 73485 AN XY: 74472

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.996

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.992

Alfa AF: 0.999 Hom.: 3507

Bravo AF: 0.982

Asia WGS AF: 0.999 AC: 3472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009568; hg19: chr11-3644815;