rs786204824
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_000894.3(LHB):c.28_39del(p.Leu10_Leu13del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LHB
NM_000894.3 inframe_deletion
NM_000894.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.14
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 19-49016690-TCAGCAGCAGCAA-T is Pathogenic according to our data. Variant chr19-49016690-TCAGCAGCAGCAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 189292.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr19-49016690-TCAGCAGCAGCAA-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHB | NM_000894.3 | c.28_39del | p.Leu10_Leu13del | inframe_deletion | 2/3 | ENST00000649238.3 | |
LHB | XM_047438832.1 | c.76_87del | p.Leu26_Leu29del | inframe_deletion | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHB | ENST00000649238.3 | c.28_39del | p.Leu10_Leu13del | inframe_deletion | 2/3 | NM_000894.3 | P1 | ||
LHB | ENST00000649284.1 | n.119_130del | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135514
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000685 AC: 10AN: 1459544Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726130
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? Cov.: 31
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Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Isolated lutropin deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2012 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at