2-48755616-GGCTGCA-GGCTGCAGCTGCAGCAGCAGCGGCTGCAGCTGCA
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_000233.4(LHCGR):c.55_56insTGCAGCCGCTGCTGCTGCAGCTGCAGC(p.Gln18_Pro19insLeuGlnProLeuLeuLeuGlnLeuGln) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000979 in 1,532,406 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 25)
Exomes 𝑓: 0.0000087 ( 0 hom. )
Consequence
LHCGR
NM_000233.4 conservative_inframe_insertion
NM_000233.4 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0830
Publications
2 publications found
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]
STON1-GTF2A1L (HGNC:30651): (STON1-GTF2A1L readthrough) STON1-GTF2A1L mRNAs are infrequent but naturally occurring read-through products of the neighboring STON1 and GTF2A1L genes. These transcripts encode fusion proteins composed of the vast majority of each of the individual elements, stonin 1 and general transcription factor IIA, 1-like. Alternative splicing results in multiple transcript variants. The significance of these read-through variants and the function of the resulting protein products have not yet been determined. [provided by RefSeq, Oct 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_000233.4
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LHCGR | NM_000233.4 | c.55_56insTGCAGCCGCTGCTGCTGCAGCTGCAGC | p.Gln18_Pro19insLeuGlnProLeuLeuLeuGlnLeuGln | conservative_inframe_insertion | Exon 1 of 11 | ENST00000294954.12 | NP_000224.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LHCGR | ENST00000294954.12 | c.55_56insTGCAGCCGCTGCTGCTGCAGCTGCAGC | p.Gln18_Pro19insLeuGlnProLeuLeuLeuGlnLeuGln | conservative_inframe_insertion | Exon 1 of 11 | 1 | NM_000233.4 | ENSP00000294954.6 | ||
| ENSG00000279956 | ENST00000602369.3 | n.55_56insTGCAGCCGCTGCTGCTGCAGCTGCAGC | non_coding_transcript_exon_variant | Exon 1 of 13 | 5 | ENSP00000473498.1 |
Frequencies
GnomAD3 genomes 0.0000198 AC: 3AN: 151850Hom.: 0 Cov.: 25 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
151850
Hom.:
Cov.:
25
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000869 AC: 12AN: 1380556Hom.: 0 Cov.: 34 AF XY: 0.0000117 AC XY: 8AN XY: 681126 show subpopulations
GnomAD4 exome
AF:
AC:
12
AN:
1380556
Hom.:
Cov.:
34
AF XY:
AC XY:
8
AN XY:
681126
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31426
American (AMR)
AF:
AC:
0
AN:
35580
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25012
East Asian (EAS)
AF:
AC:
0
AN:
35686
South Asian (SAS)
AF:
AC:
0
AN:
78996
European-Finnish (FIN)
AF:
AC:
0
AN:
37214
Middle Eastern (MID)
AF:
AC:
1
AN:
4054
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1075066
Other (OTH)
AF:
AC:
3
AN:
57522
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000198 AC: 3AN: 151850Hom.: 0 Cov.: 25 AF XY: 0.0000135 AC XY: 1AN XY: 74188 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
151850
Hom.:
Cov.:
25
AF XY:
AC XY:
1
AN XY:
74188
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41352
American (AMR)
AF:
AC:
0
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5180
South Asian (SAS)
AF:
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
AC:
0
AN:
10606
Middle Eastern (MID)
AF:
AC:
1
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67844
Other (OTH)
AF:
AC:
0
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.558
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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