2-49114197-G-T

Variant summary

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

The NM_000145.4(FSHR):​c.152+40069C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,980 control chromosomes in the GnomAD database, including 2,531 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 0.17 ( 2531 hom., cov: 32)

Consequence

FSHR
NM_000145.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0700
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FSHRNM_000145.4 linkc.152+40069C>A intron_variant ENST00000406846.7 NP_000136.2 P23945A0A1D5RMN4
FSHRNM_181446.3 linkc.152+40069C>A intron_variant NP_852111.2 P23945
FSHRXM_011532733.3 linkc.152+40069C>A intron_variant XP_011531035.1
FSHRXM_011532740.1 linkc.152+40069C>A intron_variant XP_011531042.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FSHRENST00000406846.7 linkc.152+40069C>A intron_variant 1 NM_000145.4 ENSP00000384708.2 A0A1D5RMN4

Frequencies

GnomAD3 genomes
AF:
0.169
AC:
25592
AN:
151862
Hom.:
2530
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0794
Gnomad AMI
AF:
0.223
Gnomad AMR
AF:
0.207
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.268
Gnomad FIN
AF:
0.145
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.169
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.168
AC:
25598
AN:
151980
Hom.:
2531
Cov.:
32
AF XY:
0.170
AC XY:
12656
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.0793
Gnomad4 AMR
AF:
0.207
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.245
Gnomad4 SAS
AF:
0.267
Gnomad4 FIN
AF:
0.145
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.0831
Hom.:
130
Bravo
AF:
0.167
Asia WGS
AF:
0.256
AC:
891
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.0
DANN
Benign
0.50

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: rs4971637; hg19: chr2-49341336; API