rs5030776

Positions:

• chr11-30233615-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1 PM2 PP3_Strong PP5

The ENST00000533718.2(FSHB):​c.205T>G​(p.Cys69Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FSHB ENST00000533718.2 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 5.69

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)

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM1: In a disulfide_bond (size 54) in uniprot entity FSHB_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in ENST00000533718.2
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 11-30233615-T-G is Pathogenic according to our data. Variant chr11-30233615-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 16241.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-30233615-T-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSHB	NM_001382289.1	c.205T>G	p.Cys69Gly	missense_variant	3/3	ENST00000533718.2	NP_001369218.1
ARL14EP-DT	XR_007062639.1	n.351+83275A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSHB	ENST00000533718.2	c.205T>G	p.Cys69Gly	missense_variant	3/3	1	NM_001382289.1	ENSP00000433424	P1
ARL14EP-DT	ENST00000662729.1	n.293-76762A>C		intron_variant, non_coding_transcript_variant
FSHB	ENST00000254122.8	c.205T>G	p.Cys69Gly	missense_variant	3/3	5		ENSP00000254122	P1
FSHB	ENST00000417547.1	c.205T>G	p.Cys69Gly	missense_variant	3/3	5		ENSP00000416606	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00152 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hypogonadotropic hypogonadism 24 without anosmia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Nov 25, 2010

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Pathogenic	0.99	D;D;D
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.86	.;.;D
M_CAP	Pathogenic	0.39	D
MetaRNN	Pathogenic	1.0	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	H;H;H
MutationTaster	Benign	1.0	A;A;A
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-12	D;D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D;D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		1.0	D;D;D
Vest4		0.98
MutPred		0.98		Gain of disorder (P = 0.0069);Gain of disorder (P = 0.0069);Gain of disorder (P = 0.0069);
MVP		0.99
MPC		0.90
ClinPred		1.0	D
GERP RS		6.2
Varity_R		0.97
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs5030776; hg19: chr11-30255162;