16-86513749-A-G

Position:

• chr16-86513749-A-G

Variant summary

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

The ENST00000262426.6(FOXF1):​c.*664A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,266 control chromosomes in the GnomAD database, including 50,413 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 0.81 (50393 hom., cov: 33)
  • Exomes 𝑓: 0.69 (20 hom.)
• Consequence: FOXF1 ENST00000262426.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

FOXF1 (HGNC:3809): (forkhead box F1) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in the regulation of pulmonary genes as well as embryonic development. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXF1	NM_001451.3	c.*664A>G		3_prime_UTR_variant	2/2	ENST00000262426.6	NP_001442.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXF1	ENST00000262426.6	c.*664A>G		3_prime_UTR_variant	2/2	1	NM_001451.3	ENSP00000262426	P1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123488 AN: 152074 Hom.: 50338 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.805

GnomAD4 exome AF: 0.689 AC: 51 AN: 74 Hom.: 20 Cov.: 0 AF XY: 0.682 AC XY: 30 AN XY: 44

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.688

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.812 AC: 123603 AN: 152192 Hom.: 50393 Cov.: 33 AF XY: 0.813 AC XY: 60457 AN XY: 74396

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.807

Alfa AF: 0.761 Hom.: 5349

Bravo AF: 0.823

Asia WGS AF: 0.784 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.59

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: rs1064259; hg19: chr16-86547355;