rs931250

Variant names:

• chr3-138948827-G-T
• rs931250
• NM_001040061.3:c.101-693G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040061.3(FOXL2NB):​c.101-693G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,184 control chromosomes in the GnomAD database, including 2,756 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 0.12 (2756 hom., cov: 32)
• Consequence: FOXL2NB NM_001040061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 0 publications found

Genes affected

FOXL2NB (HGNC:34428): (FOXL2 neighbor) Located in fibrillar center. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXL2NB	NM_001040061.3	c.101-693G>T		intron_variant	Intron 1 of 2	ENST00000383165.4	NP_001035150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXL2NB	ENST00000383165.4	c.101-693G>T		intron_variant	Intron 1 of 2	2	NM_001040061.3	ENSP00000372651.3
FOXL2NB	ENST00000470680.5	n.101-685G>T		intron_variant	Intron 1 of 2	3		ENSP00000418272.1
FOXL2NB	ENST00000498709.1	n.397-685G>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18652 AN: 152066 Hom.: 2744 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.123 AC: 18719 AN: 152184 Hom.: 2756 Cov.: 32 AF XY: 0.121 AC XY: 9039 AN XY: 74410

African (AFR) AF: 0.359 AC: 14879 AN: 41454

American (AMR) AF: 0.0545 AC: 834 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3472

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5178

South Asian (SAS) AF: 0.0737 AC: 356 AN: 4830

European-Finnish (FIN) AF: 0.0630 AC: 668 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1452 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0561 Hom.: 886

Bravo AF: 0.130

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.023
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs931250; hg19: chr3-138667669;