11-30233136-A-C

Variant names:

• chr11-30233136-A-C
• rs594982
• NM_001382289.1:c.160-434A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382289.1(FSHB):​c.160-434A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,976 control chromosomes in the GnomAD database, including 22,977 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 0.54 (22977 hom., cov: 33)
• Consequence: FSHB NM_001382289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSHB	NM_001382289.1	c.160-434A>C		intron_variant	Intron 2 of 2	ENST00000533718.2	NP_001369218.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSHB	ENST00000533718.2	c.160-434A>C		intron_variant	Intron 2 of 2	1	NM_001382289.1	ENSP00000433424.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81674 AN: 151858 Hom.: 22952 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81742 AN: 151976 Hom.: 22977 Cov.: 33 AF XY: 0.543 AC XY: 40338 AN XY: 74264

African (AFR) AF: 0.707 AC: 29344 AN: 41486

American (AMR) AF: 0.541 AC: 8259 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3482 AN: 5178

South Asian (SAS) AF: 0.578 AC: 2778 AN: 4808

European-Finnish (FIN) AF: 0.515 AC: 5420 AN: 10524

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29337 AN: 67930

Other (OTH) AF: 0.509 AC: 1075 AN: 2112

Alfa AF: 0.499 Hom.: 2570

Bravo AF: 0.546

Asia WGS AF: 0.580 AC: 1995 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs594982; hg19: chr11-30254683;