Variant rs2307047 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.487

Variant links:

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]

ENKUR links:

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

THNSL1 links:

ENSG00000285859 (HGNC:):

ENSG00000285859 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
ENKUR	NM_145010.4 link	c.*2029C>T		3_prime_UTR_variant	6/6	ENST00000331161.9	NP_659447.1	Q8TC29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENKUR	ENST00000331161 link	c.*2029C>T		3_prime_UTR_variant	6/6	1	NM_145010.4	ENSP00000331044.4		Q8TC29

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51149

AN:

151148

Hom.:

8784

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.259

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.338

AC XY:

25007

AN XY:

73920

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over