rs16896215

chr4-17993689-T-C

Variant summary

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

The NM_001394446.1(LCORL):c.155-20804A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,112 control chromosomes in the GnomAD database, including 5,887 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 0.24 (5887 hom., cov: 32)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCORL	NM_001394446.1	c.155-20804A>G		intron_variant		ENST00000635767.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCORL	ENST00000635767.2	c.155-20804A>G		intron_variant		5	NM_001394446.1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36994 AN: 151994 Hom.: 5855 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0910

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.244 AC: 37069 AN: 152112 Hom.: 5887 Cov.: 32 AF XY: 0.239 AC XY: 17779 AN XY: 74362

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.0910

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.237

Alfa AF: 0.199 Hom.: 1084

Bravo AF: 0.257

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.4
Dann	Benign	0.65

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: rs16896215; hg19: chr4-17995312;