rs17326656

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000233.4(LHCGR):​c.162-3854C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,148 control chromosomes in the GnomAD database, including 3,627 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3627 hom., cov: 33)

Consequence

LHCGR
NM_000233.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.444
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LHCGRNM_000233.4 linkuse as main transcriptc.162-3854C>A intron_variant ENST00000294954.12
STON1-GTF2A1LNM_001198593.2 linkuse as main transcriptc.3442-41128G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LHCGRENST00000294954.12 linkuse as main transcriptc.162-3854C>A intron_variant 1 NM_000233.4 A2P22888-1

Frequencies

GnomAD3 genomes
AF:
0.210
AC:
31960
AN:
152030
Hom.:
3625
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.319
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.271
Gnomad EAS
AF:
0.0106
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.159
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.229
Gnomad OTH
AF:
0.233
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.210
AC:
31979
AN:
152148
Hom.:
3627
Cov.:
33
AF XY:
0.202
AC XY:
15048
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.235
Gnomad4 AMR
AF:
0.171
Gnomad4 ASJ
AF:
0.271
Gnomad4 EAS
AF:
0.0106
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.159
Gnomad4 NFE
AF:
0.229
Gnomad4 OTH
AF:
0.230
Alfa
AF:
0.226
Hom.:
4173
Bravo
AF:
0.213
Asia WGS
AF:
0.0830
AC:
290
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.76
DANN
Benign
0.79

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.

Other links and lift over

dbSNP: rs17326656; hg19: chr2-48962291; API