16-86511850-C-G

Variant names:

• chr16-86511850-C-G
• rs2078304
• NM_001451.3:c.979+302C>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001451.3(FOXF1):​c.979+302C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,096 control chromosomes in the GnomAD database, including 23,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.55 (23408 hom., cov: 34)
• Consequence: FOXF1 NM_001451.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.355
• Publications: 2 publications found

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]

FOXF1 Gene-Disease associations (from GenCC):

• alveolar capillary dysplasia with misalignment of pulmonary veins

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 16-86511850-C-G is Benign according to our data. Variant chr16-86511850-C-G is described in ClinVar as Benign. ClinVar VariationId is 1273451.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF1	NM_001451.3	c.979+302C>G		intron_variant	Intron 1 of 1	ENST00000262426.6	NP_001442.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF1	ENST00000262426.6	c.979+302C>G		intron_variant	Intron 1 of 1	1	NM_001451.3	ENSP00000262426.4

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83147 AN: 151978 Hom.: 23389 Cov.: 34

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.547 AC: 83187 AN: 152096 Hom.: 23408 Cov.: 34 AF XY: 0.545 AC XY: 40544 AN XY: 74354

African (AFR) AF: 0.425 AC: 17633 AN: 41498

American (AMR) AF: 0.646 AC: 9886 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3987 AN: 5148

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5767 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39873 AN: 67958

Other (OTH) AF: 0.571 AC: 1209 AN: 2116

Alfa AF: 0.408 Hom.: 797

Bravo AF: 0.580

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 04, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2078304; hg19: chr16-86545456;