rs1392171

chr5-136295761-A-G

Variant summary

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

The NM_020389.3(TRPC7):c.963+19836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,252 control chromosomes in the GnomAD database, including 964 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 0.11 (964 hom., cov: 33)
• Consequence: TRPC7 NM_020389.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

TRPC7 (HGNC:20754): (transient receptor potential cation channel subfamily C member 7) Predicted to enable inositol 1,4,5 trisphosphate binding activity and store-operated calcium channel activity. Predicted to be involved in metal ion transport; regulation of cytosolic calcium ion concentration; and single fertilization. Predicted to act upstream of or within calcium ion transport. Predicted to be located in plasma membrane. Predicted to be part of cation channel complex. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TRPC7-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPC7	NM_020389.3	c.963+19836T>C		intron_variant		ENST00000513104.6
TRPC7-AS2	NR_133682.1	n.60-7996A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPC7	ENST00000513104.6	c.963+19836T>C		intron_variant		5	NM_020389.3	P1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17057 AN: 152134 Hom.: 965 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.112 AC: 17055 AN: 152252 Hom.: 964 Cov.: 33 AF XY: 0.110 AC XY: 8225 AN XY: 74442

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0766

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.108

Alfa AF: 0.114 Hom.: 1262

Bravo AF: 0.107

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.51
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1392171; hg19: chr5-135631449;