Variant 17-82571738-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_004514.4(FOXK2):c.777G>T(p.Pro259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00641 in 1,555,482 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0050 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0066 ( 42 hom. )

Consequence

FOXK2
NM_004514.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.181

Variant links:

Genes affected

FOXK2 (HGNC:6036): (forkhead box K2) The protein encoded by this gene contains a fork head DNA binding domain. This protein can bind to the purine-rich motifs of the HIV long terminal repeat (LTR), and to the similar purine-rich motif in the interleukin 2 (IL2) promoter. It may be involved in the regulation of viral and cellular promoter elements. [provided by RefSeq, Jul 2008]

FOXK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 17-82571738-G-T is Benign according to our data. Variant chr17-82571738-G-T is described in ClinVar as [Benign]. Clinvar id is 717485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.181 with no splicing effect.

BS2

High AC in GnomAd4 at 760 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FOXK2	NM_004514.4 linkuse as main transcript	c.777G>T	p.Pro259=	synonymous_variant	4/9	ENST00000335255.10
FOXK2	XM_047435919.1 linkuse as main transcript	c.777G>T	p.Pro259=	synonymous_variant	4/9
FOXK2	XM_047435920.1 linkuse as main transcript	c.777G>T	p.Pro259=	synonymous_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXK2	ENST00000335255.10 linkuse as main transcript	c.777G>T	p.Pro259=	synonymous_variant	4/9	1	NM_004514.4	P1	Q01167-1

Frequencies

GnomAD3 genomes

AF:

0.00502

AC:

763

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00852

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00681

Gnomad OTH

AF:

0.00863

GnomAD3 exomes

AF:

0.00484

AC:

980

AN:

202498

Hom.:

AF XY:

0.00520

AC XY:

576

AN XY:

110868

show subpopulations

Gnomad AFR exome

AF:

0.000807

Gnomad AMR exome

AF:

0.00359

Gnomad ASJ exome

AF:

0.00919

Gnomad EAS exome

AF:

0.000148

Gnomad SAS exome

AF:

0.00551

Gnomad FIN exome

AF:

0.00243

Gnomad NFE exome

AF:

0.00634

Gnomad OTH exome

AF:

0.00459

GnomAD4 exome

AF:

0.00657

AC:

9218

AN:

1403240

Hom.:

Cov.:

AF XY:

0.00658

AC XY:

4580

AN XY:

696552

show subpopulations

Gnomad4 AFR exome

AF:

0.000873

Gnomad4 AMR exome

AF:

0.00453

Gnomad4 ASJ exome

AF:

0.0101

Gnomad4 EAS exome

AF:

0.0000555

Gnomad4 SAS exome

AF:

0.00491

Gnomad4 FIN exome

AF:

0.00235

Gnomad4 NFE exome

AF:

0.00722

Gnomad4 OTH exome

AF:

0.00753

GnomAD4 genome

AF:

0.00499

AC:

760

AN:

152242

Hom.:

Cov.:

AF XY:

0.00515

AC XY:

383

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00844

Gnomad4 ASJ

AF:

0.0130

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00353

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00679

Gnomad4 OTH

AF:

0.00854

Alfa

AF:

0.00430

Hom.:

Bravo

AF:

0.00560

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	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.3

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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