6-1391873-C-T

Variant names:

• chr6-1391873-C-T
• rs1711968
• NM_001452.2:c.1171+755C>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+755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,058 control chromosomes in the GnomAD database, including 31,238 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 0.63 (31238 hom., cov: 33)
• Consequence: FOXF2 NM_001452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.1171+755C>T		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+755C>T		intron_variant	Intron 1 of 1		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96067 AN: 151940 Hom.: 31214 Cov.: 33

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.632 AC: 96137 AN: 152058 Hom.: 31238 Cov.: 33 AF XY: 0.634 AC XY: 47141 AN XY: 74324

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.593

Alfa AF: 0.566 Hom.: 23102

Bravo AF: 0.646

Asia WGS AF: 0.695 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.63
DANN	Benign	0.51

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: rs1711968; hg19: chr6-1392108;