rs724577

Variant names:

• chr4-17991787-A-C
• rs724577
• NM_001394446.1:c.155-18902T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-17991787-A-C
• chr4-17991787-A-G
• chr4-17991787-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LCORL	NM_001394446.1	c.155-18902T>G		intron_variant	Intron 1 of 7	ENST00000635767.2	NP_001381375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCORL	ENST00000635767.2	c.155-18902T>G		intron_variant	Intron 1 of 7	5	NM_001394446.1	ENSP00000490600.1

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

African (AFR) AF: 0.685 AC: 28396 AN: 41444

American (AMR) AF: 0.668 AC: 10207 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2799 AN: 5166

South Asian (SAS) AF: 0.853 AC: 4103 AN: 4808

European-Finnish (FIN) AF: 0.682 AC: 7209 AN: 10572

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50303 AN: 67946

Other (OTH) AF: 0.709 AC: 1498 AN: 2112

Alfa AF: 0.731 Hom.: 178545

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs724577; hg19: chr4-17993410;