11-30231952-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001382289.1(FSHB):​c.50G>A​(p.Cys17Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

FSHB
NM_001382289.1 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.10
Variant links:
Genes affected
FSHB (HGNC:3964): (follicle stimulating hormone subunit beta) The pituitary glycoprotein hormone family includes follicle-stimulating hormone, luteinizing hormone, chorionic gonadotropin, and thyroid-stimulating hormone. All of these glycoproteins consist of an identical alpha subunit and a hormone-specific beta subunit. This gene encodes the beta subunit of follicle-stimulating hormone. In conjunction with luteinizing hormone, follicle-stimulating hormone induces egg and sperm production. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13344112).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FSHBNM_001382289.1 linkc.50G>A p.Cys17Tyr missense_variant Exon 2 of 3 ENST00000533718.2 NP_001369218.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FSHBENST00000533718.2 linkc.50G>A p.Cys17Tyr missense_variant Exon 2 of 3 1 NM_001382289.1 ENSP00000433424.1 P01225
FSHBENST00000254122.8 linkc.50G>A p.Cys17Tyr missense_variant Exon 2 of 3 5 ENSP00000254122.3 P01225
FSHBENST00000417547.1 linkc.50G>A p.Cys17Tyr missense_variant Exon 2 of 3 5 ENSP00000416606.1 P01225
ARL14EP-DTENST00000662729.1 linkn.293-75099C>T intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.000131
AC:
20
AN:
152172
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000265
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.0000120
AC:
3
AN:
251038
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135656
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000103
AC:
15
AN:
1461618
Hom.:
0
Cov.:
32
AF XY:
0.00000963
AC XY:
7
AN XY:
727120
show subpopulations
Gnomad4 AFR exome
AF:
0.000359
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.000131
AC:
20
AN:
152172
Hom.:
0
Cov.:
33
AF XY:
0.000121
AC XY:
9
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.000265
Gnomad4 AMR
AF:
0.000393
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00143
Alfa
AF:
0.0000763
Hom.:
0
Bravo
AF:
0.000234
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Mar 15, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.50G>A (p.C17Y) alteration is located in exon 2 (coding exon 1) of the FSHB gene. This alteration results from a G to A substitution at nucleotide position 50, causing the cysteine (C) at amino acid position 17 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.075
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
17
DANN
Benign
0.78
DEOGEN2
Uncertain
0.61
D;D;D
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.063
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Benign
0.79
.;.;T
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.13
T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.2
M;M;M
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-0.97
N;N;N
REVEL
Benign
0.12
Sift
Benign
1.0
T;T;T
Sift4G
Benign
1.0
T;T;T
Polyphen
0.012
B;B;B
Vest4
0.20
MVP
0.75
MPC
0.35
ClinPred
0.047
T
GERP RS
4.0
Varity_R
0.093
gMVP
0.69

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: rs753817237; hg19: chr11-30253499; API