Variant 11-30231771-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001382289.1(FSHB):c.-37-95A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 949,642 control chromosomes in the GnomAD database, including 100,718 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 17511 hom., cov: 32)

Exomes 𝑓: 0.45 ( 83207 hom. )

Consequence

FSHB
NM_001382289.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.36

Variant links:

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]

FSHB links:

ARL14EP-DT (HGNC:55517): (ARL14EP divergent transcript)

ARL14EP-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 11-30231771-A-T is Benign according to our data. Variant chr11-30231771-A-T is described in ClinVar as [Benign]. Clinvar id is 1271122.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 linkuse as main transcript	c.-37-95A>T		intron_variant		ENST00000533718.2
ARL14EP-DT	XR_007062639.1 linkuse as main transcript	n.351+85119T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
FSHB	ENST00000533718.2 linkuse as main transcript	c.-37-95A>T	intron_variant	1	NM_001382289.1	P1
ARL14EP-DT	ENST00000662729.1 linkuse as main transcript	n.293-74918T>A	intron_variant, non_coding_transcript_variant
FSHB	ENST00000254122.8 linkuse as main transcript	c.-6-126A>T	intron_variant	5		P1
FSHB	ENST00000417547.1 linkuse as main transcript	c.-6-126A>T	intron_variant	5		P1

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72622

AN:

151868

Hom.:

17505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.640

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

GnomAD4 exome

AF:

0.449

AC:

358468

AN:

797656

Hom.:

83207

AF XY:

0.455

AC XY:

189592

AN XY:

416384

show subpopulations

Gnomad4 AFR exome

AF:

0.542

Gnomad4 AMR exome

AF:

0.369

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.656

Gnomad4 SAS exome

AF:

0.550

Gnomad4 FIN exome

AF:

0.487

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.456

GnomAD4 genome

AF:

0.478

AC:

72662

AN:

151986

Hom.:

17511

Cov.:

AF XY:

0.484

AC XY:

35947

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.541

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.640

Gnomad4 SAS

AF:

0.553

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.429

Gnomad4 OTH

AF:

0.456

Alfa

AF:

0.454

Hom.:

1952

Bravo

AF:

0.474

Asia WGS

AF:

0.542

AC:

1882

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 11, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.0010

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over