rs10508687

chr10-25037008-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

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 (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENKUR	NM_001270383.2	c.37+24104A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENKUR	ENST00000615958.4	c.37+24104A>G		intron_variant		1

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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0378

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0691

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0807 Hom.: 1176

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508687; hg19: chr10-25325937;