Genetic Variant LCORL:c.*230T>G (chr4-17845658-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001394446.1(LCORL):c.*230T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,172,896 control chromosomes in the GnomAD database, including 10,339 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 0.12 ( 1135 hom., cov: 32)

Exomes 𝑓: 0.13 ( 9204 hom. )

Consequence

LCORL
NM_001394446.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.59

Variant links:

Genes affected

LCORL (HGNC:30776): (ligand dependent nuclear receptor corepressor like) This gene encodes a transcription factor that appears to function in spermatogenesis. Polymorphisms in this gene are associated with measures of skeletal frame size and adult height. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

LCORL links:

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=-0.47).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCORL	NM_001394446.1 link	c.*230T>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000635767.2	NP_001381375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCORL	ENST00000635767 link	c.*230T>G		3_prime_UTR_variant	Exon 8 of 8	5	NM_001394446.1	ENSP00000490600.1		A0A1B0GVP4

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17606

AN:

152064

Hom.:

1131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0908

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.0556

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.138

GnomAD4 exome

AF:

0.127

AC:

129739

AN:

1020714

Hom.:

9204

Cov.:

AF XY:

0.130

AC XY:

66587

AN XY:

511802

show subpopulations

Gnomad4 AFR exome

AF:

0.0900

Gnomad4 AMR exome

AF:

0.112

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.0942

Gnomad4 SAS exome

AF:

0.227

Gnomad4 FIN exome

AF:

0.0540

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.135

GnomAD4 genome

AF:

0.116

AC:

17621

AN:

152182

Hom.:

1135

Cov.:

AF XY:

0.115

AC XY:

8578

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0908

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.137

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.0556

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.126

Hom.:

1475

Bravo

AF:

0.119

Asia WGS

AF:

0.198

AC:

689

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over