10-25037008-T-C

Variant names:

• chr10-25037008-T-C
• rs10508687
• ENST00000615958.4:c.37+24104A>G

Variant summary

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

The ENST00000615958.4(ENKUR):​c.37+24104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,108 control chromosomes in the GnomAD database, including 3,691 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 0.16 (3691 hom., cov: 32)
• Consequence: ENKUR ENST00000615958.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 4 publications found

Genes affected

ENKUR (HGNC:28388): (enkurin, TRPC channel interacting protein) This gene encodes a protein that interacts with calmodulin and several transient receptor potential canonical cation channel proteins. The encoded protein may function as an adaptor to localize signal transduction machinery to calcium channels. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ENSG00000285859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENKUR	NM_001270383.2	c.37+24104A>G		intron_variant	Intron 2 of 5		NP_001257312.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENKUR	ENST00000615958.4	c.37+24104A>G		intron_variant	Intron 2 of 5	1		ENSP00000478989.1
ENSG00000285859	ENST00000648191.1	n.336+15100T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24088 AN: 151990 Hom.: 3682 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.159 AC: 24140 AN: 152108 Hom.: 3691 Cov.: 32 AF XY: 0.151 AC XY: 11263 AN XY: 74376

African (AFR) AF: 0.406 AC: 16818 AN: 41454

American (AMR) AF: 0.0838 AC: 1281 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0378 AC: 182 AN: 4814

European-Finnish (FIN) AF: 0.0534 AC: 566 AN: 10590

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0691 AC: 4697 AN: 68008

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.0892 Hom.: 2170

Bravo AF: 0.176

Asia WGS AF: 0.0470 AC: 165 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	6.3
DANN	Benign	0.32
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10508687; hg19: chr10-25325937;