11-30233003-T-C

Variant names:

• chr11-30233003-T-C
• rs595496
• NM_001382289.1:c.160-567T>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.160-567T>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
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382289.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSHB	NM_001382289.1	MANE Select	c.160-567T>C		intron	N/A	NP_001369218.1	A0A0F7RQE8
	FSHB	NM_000510.4		c.160-567T>C		intron	N/A	NP_000501.1	P01225
	FSHB	NM_001018080.3		c.160-567T>C		intron	N/A	NP_001018090.1	A0A0F7RQE8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSHB	ENST00000533718.2	TSL:1 MANE Select	c.160-567T>C		intron	N/A	ENSP00000433424.1	P01225
	FSHB	ENST00000254122.8	TSL:5	c.160-567T>C		intron	N/A	ENSP00000254122.3	P01225
	FSHB	ENST00000417547.1	TSL:5	c.160-567T>C		intron	N/A	ENSP00000416606.1	P01225

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

African (AFR) AF: 0.532 AC: 22052 AN: 41446

American (AMR) AF: 0.438 AC: 6680 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3300 AN: 5158

South Asian (SAS) AF: 0.555 AC: 2670 AN: 4814

European-Finnish (FIN) AF: 0.514 AC: 5425 AN: 10556

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29150 AN: 67928

Other (OTH) AF: 0.454 AC: 960 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.61
PhyloP100		-0.088
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: rs595496; hg19: chr11-30254550;