rs889010

Variant names:

• chr5-136237222-C-A
• rs889010
• NM_020389.3:c.1845-5673G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-136237222-C-A
• chr5-136237222-C-G

Variant summary

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

The NM_020389.3(TRPC7):​c.1845-5673G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,942 control chromosomes in the GnomAD database, including 31,918 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 0.64 (31918 hom., cov: 31)
• Consequence: TRPC7 NM_020389.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 2 publications found

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:40937): (TRPC7 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPC7	NM_020389.3	c.1845-5673G>T		intron_variant	Intron 7 of 11	ENST00000513104.6	NP_065122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPC7	ENST00000513104.6	c.1845-5673G>T		intron_variant	Intron 7 of 11	5	NM_020389.3	ENSP00000426070.2

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96652 AN: 151826 Hom.: 31866 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.637 AC: 96752 AN: 151942 Hom.: 31918 Cov.: 31 AF XY: 0.632 AC XY: 46878 AN XY: 74214

African (AFR) AF: 0.829 AC: 34363 AN: 41466

American (AMR) AF: 0.521 AC: 7949 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3201 AN: 5136

South Asian (SAS) AF: 0.588 AC: 2828 AN: 4808

European-Finnish (FIN) AF: 0.546 AC: 5754 AN: 10540

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38592 AN: 67948

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.599 Hom.: 5813

Bravo AF: 0.646

Asia WGS AF: 0.626 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.38
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs889010; hg19: chr5-135572910;