Variant chr11-30232094-T-C 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.159+33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 1,608,472 control chromosomes in the GnomAD database, including 173,225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 18667 hom., cov: 33)

Exomes 𝑓: 0.46 ( 154558 hom. )

Consequence

FSHB
NM_001382289.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.97

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 11-30232094-T-C is Benign according to our data. Variant chr11-30232094-T-C is described in ClinVar as [Benign]. Clinvar id is 1243392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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.159+33T>C		intron_variant		ENST00000533718.2
ARL14EP-DT	XR_007062639.1 linkuse as main transcript	n.351+84796A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
FSHB	ENST00000533718.2 linkuse as main transcript	c.159+33T>C	intron_variant	1	NM_001382289.1	P1
ARL14EP-DT	ENST00000662729.1 linkuse as main transcript	n.293-75241A>G	intron_variant, non_coding_transcript_variant
FSHB	ENST00000254122.8 linkuse as main transcript	c.159+33T>C	intron_variant	5		P1
FSHB	ENST00000417547.1 linkuse as main transcript	c.159+33T>C	intron_variant	5		P1

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74863

AN:

152030

Hom.:

18654

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.519

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.514

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.471

GnomAD3 exomes

AF:

0.499

AC:

124610

AN:

249818

Hom.:

31782

AF XY:

0.499

AC XY:

67381

AN XY:

135042

show subpopulations

Gnomad AFR exome

AF:

0.555

Gnomad AMR exome

AF:

0.535

Gnomad ASJ exome

AF:

0.475

Gnomad EAS exome

AF:

0.669

Gnomad SAS exome

AF:

0.565

Gnomad FIN exome

AF:

0.501

Gnomad NFE exome

AF:

0.437

Gnomad OTH exome

AF:

0.470

GnomAD4 exome

AF:

0.456

AC:

663760

AN:

1456324

Hom.:

154558

Cov.:

AF XY:

0.460

AC XY:

333126

AN XY:

724788

show subpopulations

Gnomad4 AFR exome

AF:

0.563

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.471

Gnomad4 EAS exome

AF:

0.692

Gnomad4 SAS exome

AF:

0.568

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.429

Gnomad4 OTH exome

AF:

0.466

GnomAD4 genome

AF:

0.492

AC:

74917

AN:

152148

Hom.:

18667

Cov.:

AF XY:

0.499

AC XY:

37143

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.553

Gnomad4 AMR

AF:

0.519

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.569

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.431

Gnomad4 OTH

AF:

0.469

Alfa

AF:

0.463

Hom.:

3568

Bravo

AF:

0.496

Asia WGS

AF:

0.572

AC:

1986

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.35

DANN

Benign

0.39

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

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