Variant 19-49017115-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 XM_047438832.1(LHB):c.-338T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,613,654 control chromosomes in the GnomAD database, including 291,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 36518 hom., cov: 33)

Exomes 𝑓: 0.59 ( 254864 hom. )

Consequence

LHB
XM_047438832.1 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.62

Variant links:

Genes affected

LHB (HGNC:6584): (luteinizing hormone subunit beta) This gene is a member of the glycoprotein hormone beta chain family and encodes the beta subunit of luteinizing hormone (LH). Glycoprotein hormones are heterodimers consisting of a common alpha subunit and an unique beta subunit which confers biological specificity. LH is expressed in the pituitary gland and promotes spermatogenesis and ovulation by stimulating the testes and ovaries to synthesize steroids. The genes for the beta chains of chorionic gonadotropin and for luteinizing hormone are contiguous on chromosome 19q13.3. Mutations in this gene are associated with hypogonadism which is characterized by infertility and pseudohermaphroditism. [provided by RefSeq, Jul 2008]

LHB links:

(HGNC:):

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=-0.58).

BP6

Variant 19-49017115-A-T is Benign according to our data. Variant chr19-49017115-A-T is described in ClinVar as [Benign]. Clinvar id is 1292721.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
LHB	XM_047438832.1 linkuse as main transcript	c.-338T>A	5_prime_UTR_variant	1/2		XP_047294788.1
	use as main transcript	n.49017115A>T	intergenic_region
LHB	NM_000894.3 linkuse as main transcript	c.-34T>A	upstream_gene_variant		ENST00000649238.3	NP_000885.1	P01229A0A0F7RQE6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHB	ENST00000649238.3 linkuse as main transcript	c.-34T>A		upstream_gene_variant			NM_000894.3	ENSP00000497294.2		P01229

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102838

AN:

151992

Hom.:

36470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.655

Gnomad AMR

AF:

0.694

Gnomad ASJ

AF:

0.561

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.532

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.682

Gnomad NFE

AF:

0.593

Gnomad OTH

AF:

0.635

GnomAD3 exomes

AF:

0.604

AC:

151658

AN:

251234

Hom.:

47694

AF XY:

0.592

AC XY:

80367

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.902

Gnomad AMR exome

AF:

0.716

Gnomad ASJ exome

AF:

0.566

Gnomad EAS exome

AF:

0.326

Gnomad SAS exome

AF:

0.533

Gnomad FIN exome

AF:

0.627

Gnomad NFE exome

AF:

0.590

Gnomad OTH exome

AF:

0.592

GnomAD4 exome

AF:

0.586

AC:

855891

AN:

1461542

Hom.:

254864

Cov.:

AF XY:

0.583

AC XY:

423914

AN XY:

727088

show subpopulations

Gnomad4 AFR exome

AF:

0.909

Gnomad4 AMR exome

AF:

0.711

Gnomad4 ASJ exome

AF:

0.571

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.533

Gnomad4 FIN exome

AF:

0.629

Gnomad4 NFE exome

AF:

0.581

Gnomad4 OTH exome

AF:

0.595

GnomAD4 genome

AF:

0.677

AC:

102938

AN:

152112

Hom.:

36518

Cov.:

AF XY:

0.674

AC XY:

50104

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.894

Gnomad4 AMR

AF:

0.694

Gnomad4 ASJ

AF:

0.561

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.532

Gnomad4 FIN

AF:

0.620

Gnomad4 NFE

AF:

0.593

Gnomad4 OTH

AF:

0.632

Alfa

AF:

0.556

Hom.:

3027

Bravo

AF:

0.686

Asia WGS

AF:

0.454

AC:

1582

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	Aug 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.78

Splicing

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