16-86577785-T-G

Position:

• chr16-86577785-T-G

Variant summary

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

The ENST00000593625.1(FOXL1):​c.-162-777T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,048 control chromosomes in the GnomAD database, including 8,323 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 0.31 (8323 hom., cov: 33)
• Consequence: FOXL1 ENST00000593625.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

FOXL1 (HGNC:3817): (forkhead box L1) This gene encodes a member of the forkhead/winged helix-box (FOX) family of transcription factors. FOX transcription factors are characterized by a distinct DNA-binding forkhead domain and play critical roles in the regulation of multiple processes including metabolism, cell proliferation and gene expression during ontogenesis. [provided by RefSeq, Nov 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86577785T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXL1	ENST00000593625.1	c.-162-777T>G		intron_variant		5		ENSP00000472376.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46698 AN: 151930 Hom.: 8308 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.308 AC: 46770 AN: 152048 Hom.: 8323 Cov.: 33 AF XY: 0.313 AC XY: 23251 AN XY: 74304

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.285

Alfa AF: 0.217 Hom.: 3805

Bravo AF: 0.328

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34152738; hg19: chr16-86611391;