Variant chrX-109623948-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012282.4(KCNE5):c.*644C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.71 ( 20761 hom., 22949 hem., cov: 22)

Exomes 𝑓: 0.73 ( 6 hom. 17 hem. )

Failed GnomAD Quality Control

Consequence

KCNE5
NM_012282.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.836

Variant links:

Genes affected

KCNE5 (HGNC:6241): (potassium voltage-gated channel subfamily E regulatory subunit 5) This gene encodes a member of a family of single pass transmembrane domain proteins that function as ancillary subunits to voltage-gated potassium channels. Members of this family affect diverse processes in potassium channel regulation, including ion selectivity, voltage dependence, and anterograde recycling from the plasma membrane. Variants of this gene are associated with idiopathic ventricular fibrillation and Brugada syndrome. [provided by RefSeq, Nov 2016]

KCNE5 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=-0.83).

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNE5	NM_012282.4 linkuse as main transcript	c.*644C>T		3_prime_UTR_variant	1/1	ENST00000372101.3	NP_036414.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNE5	ENST00000372101.3 linkuse as main transcript	c.*644C>T		3_prime_UTR_variant	1/1		NM_012282.4	ENSP00000361173	P1

Frequencies

GnomAD3 genomes

AF:

0.714

AC:

78703

AN:

110171

Hom.:

20763

Cov.:

AF XY:

0.707

AC XY:

22893

AN XY:

32389

show subpopulations

Gnomad AFR

AF:

0.887

Gnomad AMI

AF:

0.828

Gnomad AMR

AF:

0.767

Gnomad ASJ

AF:

0.646

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.748

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.761

Gnomad NFE

AF:

0.614

Gnomad OTH

AF:

0.722

GnomAD4 exome

AF:

0.729

AC:

AN:

Hom.:

Cov.:

AF XY:

0.850

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.714

Gnomad4 NFE exome

AF:

0.690

Gnomad4 OTH exome

AF:

0.778

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.714

AC:

78754

AN:

110226

Hom.:

20761

Cov.:

AF XY:

0.707

AC XY:

22949

AN XY:

32454

show subpopulations

Gnomad4 AFR

AF:

0.887

Gnomad4 AMR

AF:

0.767

Gnomad4 ASJ

AF:

0.646

Gnomad4 EAS

AF:

0.919

Gnomad4 SAS

AF:

0.750

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.614

Gnomad4 OTH

AF:

0.722

Alfa

AF:

0.660

Hom.:

29832

Bravo

AF:

0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

DANN

Benign

0.74

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