6-1394884-G-A

Variant names:

• chr6-1394884-G-A
• rs45600838
• NM_001452.2:c.*25G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001452.2(FOXF2):​c.*25G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 1,611,950 control chromosomes in the GnomAD database, including 98 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 0.0070 (7 hom., cov: 33)
  • Exomes 𝑓: 0.0092 (91 hom.)
• Consequence: FOXF2 NM_001452.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS2: High AC in GnomAd4 at 1072 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.*25G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000645481.2	NP_001443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.*25G>A		3_prime_UTR_variant	Exon 2 of 2		NM_001452.2	ENSP00000496415.1

Frequencies

GnomAD3 genomes AF: 0.00705 AC: 1072 AN: 152148 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.00113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.00526

GnomAD2 exomes AF: 0.00842 AC: 2115 AN: 251286 AF XY: 0.00875

Gnomad AFR exome AF: 0.000861

Gnomad AMR exome AF: 0.00139

Gnomad ASJ exome AF: 0.00606

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.0124

Gnomad NFE exome AF: 0.0135

Gnomad OTH exome AF: 0.00978

GnomAD4 exome AF: 0.00916 AC: 13369 AN: 1459684 Hom.: 91 Cov.: 30 AF XY: 0.00928 AC XY: 6738 AN XY: 726314

African (AFR) AF: 0.00111 AC: 37 AN: 33428

American (AMR) AF: 0.00143 AC: 64 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 143 AN: 26116

East Asian (EAS) AF: 0.0000504 AC: 2 AN: 39682

South Asian (SAS) AF: 0.00493 AC: 425 AN: 86220

European-Finnish (FIN) AF: 0.0145 AC: 774 AN: 53248

Middle Eastern (MID) AF: 0.00173 AC: 10 AN: 5764

European-Non Finnish (NFE) AF: 0.0103 AC: 11453 AN: 1110208

Other (OTH) AF: 0.00765 AC: 461 AN: 60298

GnomAD4 genome AF: 0.00704 AC: 1072 AN: 152266 Hom.: 7 Cov.: 33 AF XY: 0.00674 AC XY: 502 AN XY: 74468

African (AFR) AF: 0.00113 AC: 47 AN: 41550

American (AMR) AF: 0.00131 AC: 20 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4822

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 836 AN: 68008

Other (OTH) AF: 0.00520 AC: 11 AN: 2114

Alfa AF: 0.00980 Hom.: 2

Bravo AF: 0.00563

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.043
DANN	Benign	0.89
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

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: rs45600838; hg19: chr6-1395119;