rs4494802

Variant summary

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

The NM_000145.4(FSHR):​c.375-3370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,256 control chromosomes in the GnomAD database, including 844 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 0.093 ( 844 hom., cov: 33)

Consequence

FSHR
NM_000145.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05
Variant links:
Genes affected
FSHR (HGNC:3969): (follicle stimulating hormone receptor) The protein encoded by this gene belongs to family 1 of G-protein coupled receptors. It is the receptor for follicle stimulating hormone and functions in gonad development. Mutations in this gene cause ovarian dysgenesis type 1, and also ovarian hyperstimulation syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FSHRNM_000145.4 linkuse as main transcriptc.375-3370A>G intron_variant ENST00000406846.7 NP_000136.2 P23945A0A1D5RMN4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FSHRENST00000406846.7 linkuse as main transcriptc.375-3370A>G intron_variant 1 NM_000145.4 ENSP00000384708.2 A0A1D5RMN4

Frequencies

GnomAD3 genomes
AF:
0.0929
AC:
14138
AN:
152138
Hom.:
841
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0242
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.0829
Gnomad ASJ
AF:
0.132
Gnomad EAS
AF:
0.169
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.137
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.120
Gnomad OTH
AF:
0.102
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0930
AC:
14159
AN:
152256
Hom.:
844
Cov.:
33
AF XY:
0.0950
AC XY:
7072
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0241
Gnomad4 AMR
AF:
0.0833
Gnomad4 ASJ
AF:
0.132
Gnomad4 EAS
AF:
0.170
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.137
Gnomad4 NFE
AF:
0.120
Gnomad4 OTH
AF:
0.108
Alfa
AF:
0.108
Hom.:
149
Bravo
AF:
0.0867
Asia WGS
AF:
0.141
AC:
491
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.11
DANN
Benign
0.71

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: rs4494802; hg19: chr2-49221146; API