rs2307047

chr10-24982341-G-Achr10-24982341-G-Cchr10-24982341-G-T

Variant summary

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

The NM_145010.4(ENKUR):c.*2029C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,340 control chromosomes in the GnomAD database, including 8,792 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 0.34 (8788 hom., cov: 31)
  • Exomes 𝑓: 0.28 (4 hom.)
• Consequence: ENKUR NM_145010.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

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]

THNSL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENKUR	NM_145010.4	c.*2029C>T		3_prime_UTR_variant	6/6	ENST00000331161.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENKUR	ENST00000331161.9	c.*2029C>T		3_prime_UTR_variant	6/6	1	NM_145010.4	P4
ENKUR	ENST00000615958.4	c.*2029C>T		3_prime_UTR_variant	6/6	1
ENKUR	ENST00000496261.6	c.*590C>T		3_prime_UTR_variant, NMD_transcript_variant	7/7	1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51149 AN: 151148 Hom.: 8784 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.278 AC: 20 AN: 72 Hom.: 4 Cov.: 0 AF XY: 0.259 AC XY: 14 AN XY: 54

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.259

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.338 AC: 51174 AN: 151268 Hom.: 8788 Cov.: 31 AF XY: 0.338 AC XY: 25007 AN XY: 73920

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.339

Alfa AF: 0.325 Hom.: 13730

Bravo AF: 0.350

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.4
Dann	Benign	0.73

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: rs2307047; hg19: chr10-25271270;