16-86511850-C-T

Position:

• chr16-86511850-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001451.3(FOXF1):​c.979+302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,132 control chromosomes in the GnomAD database, including 274 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.047 (274 hom., cov: 34)
• Consequence: FOXF1 NM_001451.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.355

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 16-86511850-C-T is Benign according to our data. Variant chr16-86511850-C-T is described in ClinVar as [Benign]. Clinvar id is 1252327.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXF1	NM_001451.3	c.979+302C>T		intron_variant		ENST00000262426.6	NP_001442.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXF1	ENST00000262426.6	c.979+302C>T		intron_variant		1	NM_001451.3	ENSP00000262426.4

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7073 AN: 152014 Hom.: 273 Cov.: 34

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0466 AC: 7088 AN: 152132 Hom.: 274 Cov.: 34 AF XY: 0.0491 AC XY: 3653 AN XY: 74364

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0260

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0263 Hom.: 797

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 12, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.6
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

Other links and lift over

dbSNP: rs2078304; hg19: chr16-86545456;