GeneBe

NM_013409.3:c.953-184A>C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_013409.3(FST):​c.953-184A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000279 in 1,432,296 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 29)
Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

FST
NM_013409.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

13 publications found
Variant links:
Genes affected
FST (HGNC:3971): (follistatin) Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. The single FST gene encodes two isoforms, FST317 and FST344 containing 317 and 344 amino acids respectively, resulting from alternative splicing of the precursor mRNA. In a study in which 37 candidate genes were tested for linkage and association with polycystic ovary syndrome (PCOS) or hyperandrogenemia in 150 families, evidence was found for linkage between PCOS and follistatin. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FSTNM_013409.3 linkc.953-184A>C intron_variant Intron 5 of 5 ENST00000256759.8 NP_037541.1 P19883-1A0A024QZU6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FSTENST00000256759.8 linkc.953-184A>C intron_variant Intron 5 of 5 1 NM_013409.3 ENSP00000256759.3 P19883-1
FSTENST00000396947.7 linkc.*79A>C 3_prime_UTR_variant Exon 6 of 6 5 ENSP00000380151.2 P19883-2
FSTENST00000497789.2 linkc.*79A>C 3_prime_UTR_variant Exon 3 of 3 2 ENSP00000426971.1 H0YAF9
FSTENST00000504226.5 linkc.566-184A>C intron_variant Intron 3 of 3 3 ENSP00000426315.1 H0YA75

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
0.00000279
AC:
4
AN:
1432296
Hom.:
0
Cov.:
30
AF XY:
0.00000140
AC XY:
1
AN XY:
712630
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
31336
American (AMR)
AF:
0.00
AC:
0
AN:
37278
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25080
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39560
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81078
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53128
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5634
European-Non Finnish (NFE)
AF:
0.00000364
AC:
4
AN:
1100022
Other (OTH)
AF:
0.00
AC:
0
AN:
59180
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
29
Alfa
AF:
0.00
Hom.:
802

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.011
DANN
Benign
0.17
PhyloP100
-1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs722910; hg19: chr5-52781597; API