rs45600838

Positions:

• chr6-1394884-G-A
• chr6-1394884-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	Protein	UniProt
FOXF2	NM_001452.2	c.*25G>A		3_prime_UTR_variant	2/2	ENST00000645481.2	NP_001443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXF2	ENST00000645481.2	c.*25G>A		3_prime_UTR_variant	2/2		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

GnomAD3 exomes AF: 0.00842 AC: 2115 AN: 251286 Hom.: 20 AF XY: 0.00875 AC XY: 1188 AN XY: 135836

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 SAS exome AF: 0.00434

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

Gnomad4 AFR exome AF: 0.00111

Gnomad4 AMR exome AF: 0.00143

Gnomad4 ASJ exome AF: 0.00548

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00493

Gnomad4 FIN exome AF: 0.0145

Gnomad4 NFE exome AF: 0.0103

Gnomad4 OTH exome AF: 0.00765

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

Gnomad4 AFR AF: 0.00113

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.00520

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

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: rs45600838; hg19: chr6-1395119;