ENST00000496261.6:n.*590C>T

Variant names:

• chr10-24982341-G-A
• rs2307047
• ENST00000496261.6:n.*590C>T

Variant summary

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

The ENST00000496261.6(ENKUR):​n.*590C>T variant causes a non coding transcript exon 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 ENST00000496261.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 1 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:):

THNSL1 (HGNC:26160): (threonine synthase like 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ENKUR	NM_145010.4	c.*2029C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000331161.9	NP_659447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENKUR	ENST00000331161.9	c.*2029C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_145010.4	ENSP00000331044.4

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.259 AC: 14 AN: 54

Other (OTH) AF: 0.300 AC: 3 AN: 10

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

African (AFR) AF: 0.307 AC: 12636 AN: 41148

American (AMR) AF: 0.414 AC: 6287 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1061 AN: 3456

East Asian (EAS) AF: 0.482 AC: 2469 AN: 5120

South Asian (SAS) AF: 0.426 AC: 2037 AN: 4782

European-Finnish (FIN) AF: 0.314 AC: 3296 AN: 10512

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22214 AN: 67744

Other (OTH) AF: 0.339 AC: 712 AN: 2102

Alfa AF: 0.330 Hom.: 23622

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
PhyloP100		-0.49
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: rs2307047; hg19: chr10-25271270;