rs925098

chr4-17918188-G-Achr4-17918188-G-C

Variant summary

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

The NM_001394446.1(LCORL):c.431-8843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,112 control chromosomes in the GnomAD database, including 37,521 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 0.70 (37521 hom., cov: 33)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCORL	NM_001394446.1	c.431-8843C>T		intron_variant		ENST00000635767.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCORL	ENST00000635767.2	c.431-8843C>T		intron_variant		5	NM_001394446.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106281 AN: 151994 Hom.: 37473 Cov.: 33

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.699 AC: 106386 AN: 152112 Hom.: 37521 Cov.: 33 AF XY: 0.696 AC XY: 51759 AN XY: 74358

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.695

Alfa AF: 0.730 Hom.: 66405

Bravo AF: 0.688

Asia WGS AF: 0.698 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.8
Dann	Benign	0.73

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: rs925098; hg19: chr4-17919811;