rs10834677

Positions:

• chr11-3633446-C-A
• chr11-3633446-C-G
• chr11-3633446-C-T

Variant summary

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

The NR_002720.2(TRPC2):​n.285-846C>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 0.51 in 152,118 control chromosomes in the GnomAD database, including 23,903 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 0.51 (23903 hom., cov: 32)
• Consequence: TRPC2 NR_002720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPC2	NR_002720.2	n.285-846C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPC2	ENST00000451043.7	n.1761-846C>A		intron_variant, non_coding_transcript_variant
TRPC2	ENST00000526541.1	n.261-846C>A		intron_variant, non_coding_transcript_variant		1
TRPC2	ENST00000696867.1	n.361-846C>A		intron_variant, non_coding_transcript_variant
TRPC2	ENST00000696868.1	n.439-846C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77611 AN: 152000 Hom.: 23898 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.510 AC: 77612 AN: 152118 Hom.: 23903 Cov.: 32 AF XY: 0.516 AC XY: 38387 AN XY: 74350

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.500

Alfa AF: 0.603 Hom.: 15625

Bravo AF: 0.484

Asia WGS AF: 0.609 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
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: rs10834677; hg19: chr11-3654676;