Variant 2-10913614-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002236.5(KCNF1):c.1188C>T(p.Ile396Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,612,932 control chromosomes in the GnomAD database, including 314,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.55 ( 23870 hom., cov: 32)

Exomes 𝑓: 0.63 ( 290590 hom. )

Consequence

KCNF1
NM_002236.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.204

Variant links:

Genes affected

KCNF1 (HGNC:6246): (potassium voltage-gated channel modifier subfamily F member 1) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, subfamily F. This gene is intronless and expressed in all tissues tested, including the heart, skeletal muscle, brain, kidney, and pancreas. [provided by RefSeq, Jul 2008]

KCNF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 2-10913614-C-T is Benign according to our data. Variant chr2-10913614-C-T is described in ClinVar as [Benign]. Clinvar id is 1294515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.204 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNF1	NM_002236.5 linkuse as main transcript	c.1188C>T	p.Ile396Ile	synonymous_variant	1/1	ENST00000295082.3	NP_002227.2	Q9H3M0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNF1	ENST00000295082.3 linkuse as main transcript	c.1188C>T	p.Ile396Ile	synonymous_variant	1/1	6	NM_002236.5	ENSP00000295082.1		Q9H3M0

Frequencies

GnomAD3 genomes

AF:

0.547

AC:

83111

AN:

151942

Hom.:

23874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.648

Gnomad OTH

AF:

0.571

GnomAD3 exomes

AF:

0.576

AC:

144441

AN:

250586

Hom.:

42776

AF XY:

0.585

AC XY:

79307

AN XY:

135530

show subpopulations

Gnomad AFR exome

AF:

0.360

Gnomad AMR exome

AF:

0.457

Gnomad ASJ exome

AF:

0.651

Gnomad EAS exome

AF:

0.533

Gnomad SAS exome

AF:

0.541

Gnomad FIN exome

AF:

0.584

Gnomad NFE exome

AF:

0.652

Gnomad OTH exome

AF:

0.587

GnomAD4 exome

AF:

0.627

AC:

915387

AN:

1460872

Hom.:

290590

Cov.:

AF XY:

0.625

AC XY:

454569

AN XY:

726830

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.467

Gnomad4 ASJ exome

AF:

0.647

Gnomad4 EAS exome

AF:

0.494

Gnomad4 SAS exome

AF:

0.540

Gnomad4 FIN exome

AF:

0.591

Gnomad4 NFE exome

AF:

0.655

Gnomad4 OTH exome

AF:

0.609

GnomAD4 genome

AF:

0.547

AC:

83118

AN:

152060

Hom.:

23870

Cov.:

AF XY:

0.541

AC XY:

40220

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.371

Gnomad4 AMR

AF:

0.536

Gnomad4 ASJ

AF:

0.642

Gnomad4 EAS

AF:

0.510

Gnomad4 SAS

AF:

0.528

Gnomad4 FIN

AF:

0.574

Gnomad4 NFE

AF:

0.648

Gnomad4 OTH

AF:

0.565

Alfa

AF:

0.608

Hom.:

29296

Bravo

AF:

0.536

Asia WGS

AF:

0.478

AC:

1662

AN:

3478

EpiCase

AF:

0.647

EpiControl

AF:

0.655

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 03, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

2.0

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over