rs550312

Variant names:

• chr11-30231642-T-G
• rs550312
• NM_001382289.1:c.-37-224T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-30231642-T-G
• chr11-30231642-T-C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001382289.1(FSHB):​c.-37-224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,024 control chromosomes in the GnomAD database, including 17,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17529 hom., cov: 33)
• Consequence: FSHB NM_001382289.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0740
• Publications: 4 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-30231642-T-G is Benign according to our data. Variant chr11-30231642-T-G is described in ClinVar as Benign. ClinVar VariationId is 1220841.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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.-37-224T>G		intron	N/A	NP_001369218.1	A0A0F7RQE8
	FSHB	NM_000510.4		c.-6-255T>G		intron	N/A	NP_000501.1	P01225
	FSHB	NM_001018080.3		c.-6-255T>G		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.-37-224T>G		intron	N/A	ENSP00000433424.1	P01225
	FSHB	ENST00000254122.8	TSL:5	c.-6-255T>G		intron	N/A	ENSP00000254122.3	P01225
	FSHB	ENST00000417547.1	TSL:5	c.-6-255T>G		intron	N/A	ENSP00000416606.1	P01225

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72653 AN: 151906 Hom.: 17523 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.478 AC: 72693 AN: 152024 Hom.: 17529 Cov.: 33 AF XY: 0.484 AC XY: 35951 AN XY: 74294

African (AFR) AF: 0.541 AC: 22430 AN: 41476

American (AMR) AF: 0.439 AC: 6699 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3466

East Asian (EAS) AF: 0.640 AC: 3309 AN: 5172

South Asian (SAS) AF: 0.553 AC: 2664 AN: 4814

European-Finnish (FIN) AF: 0.514 AC: 5431 AN: 10562

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

European-Non Finnish (NFE) AF: 0.429 AC: 29163 AN: 67958

Other (OTH) AF: 0.455 AC: 959 AN: 2106

Alfa AF: 0.454 Hom.: 1951

Bravo AF: 0.474

Asia WGS AF: 0.541 AC: 1878 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		0.074
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: rs550312; hg19: chr11-30253189;