rs11924939

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_023067.4(FOXL2):​c.-232G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 610,648 control chromosomes in the GnomAD database, including 11,713 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 0.15 ( 2347 hom., cov: 33)
Exomes 𝑓: 0.19 ( 9366 hom. )

Consequence

FOXL2
NM_023067.4 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.402
Variant links:
Genes affected
FOXL2 (HGNC:1092): (forkhead box L2) This gene encodes a forkhead transcription factor. The protein contains a fork-head DNA-binding domain and may play a role in ovarian development and function. Expansion of a polyalanine repeat region and other mutations in this gene are a cause of blepharophimosis syndrome and premature ovarian failure 3. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FOXL2NM_023067.4 linkuse as main transcriptc.-232G>A 5_prime_UTR_variant 1/1 ENST00000648323.1 NP_075555.1 P58012Q53ZD3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FOXL2ENST00000648323.1 linkuse as main transcriptc.-232G>A 5_prime_UTR_variant 1/1 NM_023067.4 ENSP00000497217.1 P58012

Frequencies

GnomAD3 genomes
AF:
0.152
AC:
23083
AN:
152106
Hom.:
2347
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0443
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.145
Gnomad ASJ
AF:
0.249
Gnomad EAS
AF:
0.00155
Gnomad SAS
AF:
0.0530
Gnomad FIN
AF:
0.181
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.172
GnomAD4 exome
AF:
0.185
AC:
85027
AN:
458424
Hom.:
9366
Cov.:
6
AF XY:
0.182
AC XY:
43272
AN XY:
237936
show subpopulations
Gnomad4 AFR exome
AF:
0.0454
Gnomad4 AMR exome
AF:
0.131
Gnomad4 ASJ exome
AF:
0.244
Gnomad4 EAS exome
AF:
0.000334
Gnomad4 SAS exome
AF:
0.0631
Gnomad4 FIN exome
AF:
0.181
Gnomad4 NFE exome
AF:
0.225
Gnomad4 OTH exome
AF:
0.183
GnomAD4 genome
AF:
0.152
AC:
23075
AN:
152224
Hom.:
2347
Cov.:
33
AF XY:
0.147
AC XY:
10964
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0442
Gnomad4 AMR
AF:
0.145
Gnomad4 ASJ
AF:
0.249
Gnomad4 EAS
AF:
0.00155
Gnomad4 SAS
AF:
0.0528
Gnomad4 FIN
AF:
0.181
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.170
Alfa
AF:
0.192
Hom.:
632
Bravo
AF:
0.148
Asia WGS
AF:
0.0270
AC:
94
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
17
DANN
Benign
0.95

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11924939; hg19: chr3-138665796; COSMIC: COSV57728323; COSMIC: COSV57728323; API