rs4073366
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000233.4(LHCGR):c.161+28G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,431,042 control chromosomes in the GnomAD database, including 21,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2275 hom., cov: 32)
Exomes 𝑓: 0.16 ( 19170 hom. )
Consequence
LHCGR
NM_000233.4 intron
NM_000233.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0630
Genes affected
LHCGR (HGNC:6585): (luteinizing hormone/choriogonadotropin receptor) This gene encodes the receptor for both luteinizing hormone and choriogonadotropin. This receptor belongs to the G-protein coupled receptor 1 family, and its activity is mediated by G proteins which activate adenylate cyclase. Mutations in this gene result in disorders of male secondary sexual character development, including familial male precocious puberty, also known as testotoxicosis, hypogonadotropic hypogonadism, Leydig cell adenoma with precocious puberty, and male pseudohermaphtoditism with Leydig cell hypoplasia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 2-48755483-C-G is Benign according to our data. Variant chr2-48755483-C-G is described in ClinVar as [Benign]. Clinvar id is 1278671.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-48755483-C-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHCGR | NM_000233.4 | c.161+28G>C | intron_variant | ENST00000294954.12 | |||
STON1-GTF2A1L | NM_001198593.2 | c.3442-20797C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHCGR | ENST00000294954.12 | c.161+28G>C | intron_variant | 1 | NM_000233.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.160 AC: 24357AN: 152056Hom.: 2267 Cov.: 32
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GnomAD3 exomes AF: 0.187 AC: 26433AN: 141026Hom.: 3204 AF XY: 0.174 AC XY: 13232AN XY: 75932
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GnomAD4 exome AF: 0.165 AC: 210580AN: 1278868Hom.: 19170 Cov.: 18 AF XY: 0.161 AC XY: 102423AN XY: 634988
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GnomAD4 genome ? AF: 0.160 AC: 24376AN: 152174Hom.: 2275 Cov.: 32 AF XY: 0.162 AC XY: 12022AN XY: 74386
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at