chr2-49154560-T-C

Position:

• chr2-49154560-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000634588.1(ENSG00000282890):​n.492+208155T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: 18)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSHR	NM_000145.4			upstream_gene_variant		ENST00000406846.7	NP_000136.2
FSHR	NM_181446.3			upstream_gene_variant			NP_852111.2
FSHR	XM_011532733.3			upstream_gene_variant			XP_011531035.1
FSHR	XM_011532740.1			upstream_gene_variant			XP_011531042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634588.1	n.492+208155T>C		intron_variant, non_coding_transcript_variant		5
FSHR	ENST00000406846.7			upstream_gene_variant		1	NM_000145.4	ENSP00000384708	P1
FSHR	ENST00000419927.1			upstream_gene_variant		1		ENSP00000405775

Frequencies

GnomAD3 genomes Cov.: 18

GnomAD4 exome AF: 0.000101 AC: 22 AN: 218214 Hom.: 0 Cov.: 0 AF XY: 0.000140 AC XY: 16 AN XY: 114492

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000455

Gnomad4 ASJ exome AF: 0.000137

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000203

Gnomad4 FIN exome AF: 0.0000785

Gnomad4 NFE exome AF: 0.0000836

Gnomad4 OTH exome AF: 0.000182

GnomAD4 genome Cov.: 18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2349718; hg19: chr2-49381699;