Variant 6-1394796-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001452.2(FOXF2):c.1272C>T(p.Ser424=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 1,613,998 control chromosomes in the GnomAD database, including 159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0096 ( 10 hom., cov: 33)

Exomes 𝑓: 0.013 ( 149 hom. )

Consequence

FOXF2
NM_001452.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.314

Variant links:

Genes affected

FOXF2 (HGNC:3810): (forkhead box F2) FOXF2 encodes forkhead box F2, one of many human homologues of the Drosophila melanogaster transcription factor forkhead. FOXF2 is expressed in lung and placenta, and has been shown to transcriptionally activate several lung-specific genes. [provided by RefSeq, Jul 2008]

FOXF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 6-1394796-C-T is Benign according to our data. Variant chr6-1394796-C-T is described in ClinVar as [Benign]. Clinvar id is 2656172.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.314 with no splicing effect.

BS2

High AC in GnomAd4 at 1462 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXF2	NM_001452.2 linkuse as main transcript	c.1272C>T	p.Ser424=	synonymous_variant	2/2	ENST00000645481.2	NP_001443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2 linkuse as main transcript	c.1272C>T	p.Ser424=	synonymous_variant	2/2		NM_001452.2	ENSP00000496415	P1

Frequencies

GnomAD3 genomes

AF:

0.00961

AC:

1462

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00215

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00270

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0143

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00973

AC:

2447

AN:

251492

Hom.:

AF XY:

0.00979

AC XY:

1331

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00199

Gnomad FIN exome

AF:

0.0313

Gnomad NFE exome

AF:

0.0137

Gnomad OTH exome

AF:

0.00977

GnomAD4 exome

AF:

0.0126

AC:

18363

AN:

1461778

Hom.:

149

Cov.:

AF XY:

0.0122

AC XY:

8900

AN XY:

727196

show subpopulations

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.00145

Gnomad4 ASJ exome

AF:

0.00233

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00246

Gnomad4 FIN exome

AF:

0.0303

Gnomad4 NFE exome

AF:

0.0142

Gnomad4 OTH exome

AF:

0.00985

GnomAD4 genome

AF:

0.00960

AC:

1462

AN:

152220

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

770

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.00214

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00270

Gnomad4 FIN

AF:

0.0322

Gnomad4 NFE

AF:

0.0143

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00974

Hom.:

Bravo

AF:

0.00690

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0121

EpiControl

AF:

0.00978

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

FOXF2: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

1.6

DANN

Benign

0.65

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