rs16896068

Variant names:

• chr4-17943217-G-A
• rs16896068
• NM_001394446.1:c.430+18686C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-17943217-G-A
• chr4-17943217-G-T

Variant summary

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

The NM_001394446.1(LCORL):​c.430+18686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,932 control chromosomes in the GnomAD database, including 6,199 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 0.25 (6199 hom., cov: 31)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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 (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCORL	NM_001394446.1	c.430+18686C>T		intron_variant	Intron 4 of 7	ENST00000635767.2	NP_001381375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCORL	ENST00000635767.2	c.430+18686C>T		intron_variant	Intron 4 of 7	5	NM_001394446.1	ENSP00000490600.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37731 AN: 151814 Hom.: 6167 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37809 AN: 151932 Hom.: 6199 Cov.: 31 AF XY: 0.244 AC XY: 18146 AN XY: 74266

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.0916

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.243

Alfa AF: 0.169 Hom.: 3937

Bravo AF: 0.263

Asia WGS AF: 0.242 AC: 845 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	0.45
DANN	Benign	0.78

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: rs16896068; hg19: chr4-17944840;