rs732835

Variant names:

• chr6-1392765-G-C
• rs732835
• NM_001452.2:c.1171+1647G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-1392765-G-C
• chr6-1392765-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001452.2(FOXF2):​c.1171+1647G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,194 control chromosomes in the GnomAD database, including 3,028 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 0.19 (3028 hom., cov: 33)
• Consequence: FOXF2 NM_001452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.1171+1647G>C		intron_variant	Intron 1 of 1	ENST00000645481.2	NP_001443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.1171+1647G>C		intron_variant	Intron 1 of 1		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28534 AN: 152074 Hom.: 3027 Cov.: 33

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.239

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.188 AC: 28539 AN: 152194 Hom.: 3028 Cov.: 33 AF XY: 0.185 AC XY: 13745 AN XY: 74400

Gnomad4 AFR AF: 0.0971

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.245

Alfa AF: 0.116 Hom.: 204

Bravo AF: 0.190

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.022
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs732835; hg19: chr6-1393000;