11-30233003-T-C

Variant summary

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

The NM_001382289.1(FSHB):c.160-567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,948 control chromosomes in the GnomAD database, including 17,315 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 0.48 (17315 hom., cov: 32)
• Consequence: FSHB NM_001382289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSHB	NM_001382289.1	c.160-567T>C		intron_variant		ENST00000533718.2
ARL14EP-DT	XR_007062639.1	n.351+83887A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSHB	ENST00000533718.2	c.160-567T>C		intron_variant		1	NM_001382289.1	P1
ARL14EP-DT	ENST00000662729.1	n.293-76150A>G		intron_variant, non_coding_transcript_variant
FSHB	ENST00000254122.8	c.160-567T>C		intron_variant		5		P1
FSHB	ENST00000417547.1	c.160-567T>C		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72242 AN: 151830 Hom.: 17310 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.476 AC: 72277 AN: 151948 Hom.: 17315 Cov.: 32 AF XY: 0.481 AC XY: 35735 AN XY: 74246

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.454

Alfa AF: 0.322 Hom.: 808

Bravo AF: 0.471

Asia WGS AF: 0.543 AC: 1875 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.0
Dann	Benign	0.61

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: rs595496; hg19: chr11-30254550;