rs2055571

chr2-49117675-G-Achr2-49117675-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000145.4(FSHR):c.152+36591C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,040 control chromosomes in the GnomAD database, including 18,057 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 0.47 (18057 hom., cov: 32)
• Consequence: FSHR NM_000145.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSHR	NM_000145.4	c.152+36591C>T		intron_variant		ENST00000406846.7
FSHR	NM_181446.3	c.152+36591C>T		intron_variant
FSHR	XM_011532733.3	c.152+36591C>T		intron_variant
FSHR	XM_011532740.1	c.152+36591C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSHR	ENST00000406846.7	c.152+36591C>T		intron_variant		1	NM_000145.4	P1
	ENST00000634588.1	n.492+171270G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72065 AN: 151924 Hom.: 18008 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.485

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.475 AC: 72168 AN: 152040 Hom.: 18057 Cov.: 32 AF XY: 0.478 AC XY: 35473 AN XY: 74276

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.486

Alfa AF: 0.421 Hom.: 1796

Bravo AF: 0.496

Asia WGS AF: 0.621 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.38

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

Other links and lift over

dbSNP: rs2055571; hg19: chr2-49344814;