rs724577

chr4-17991787-A-Cchr4-17991787-A-Gchr4-17991787-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394446.1(LCORL):c.155-18902T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,002 control chromosomes in the GnomAD database, including 38,695 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 0.71 (38695 hom., cov: 31)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCORL	NM_001394446.1	c.155-18902T>G		intron_variant		ENST00000635767.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCORL	ENST00000635767.2	c.155-18902T>G		intron_variant		5	NM_001394446.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107976 AN: 151884 Hom.: 38649 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.707

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.711 AC: 108081 AN: 152002 Hom.: 38695 Cov.: 31 AF XY: 0.708 AC XY: 52573 AN XY: 74276

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.709

Alfa AF: 0.738 Hom.: 87741

Bravo AF: 0.702

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.37

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

Other links and lift over

dbSNP: rs724577; hg19: chr4-17993410;