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. The variant received -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
• Publications: 40 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCORL	NM_001394446.1	MANE Select	c.430+18686C>T		intron	N/A	NP_001381375.1	A0A1B0GVP4
	LCORL	NM_001166139.2		c.430+18686C>T		intron	N/A	NP_001159611.1	Q8N3X6-1
	LCORL	NM_001365658.1		c.-51+17048C>T		intron	N/A	NP_001352587.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCORL	ENST00000635767.2	TSL:5 MANE Select	c.430+18686C>T		intron	N/A	ENSP00000490600.1	A0A1B0GVP4
	LCORL	ENST00000326877.8	TSL:1	c.430+18686C>T		intron	N/A	ENSP00000317566.3	Q8N3X6-3
	LCORL	ENST00000382226.5	TSL:5	c.430+18686C>T		intron	N/A	ENSP00000371661.5	Q8N3X6-1

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

African (AFR) AF: 0.464 AC: 19223 AN: 41388

American (AMR) AF: 0.201 AC: 3061 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 979 AN: 3464

East Asian (EAS) AF: 0.138 AC: 711 AN: 5164

South Asian (SAS) AF: 0.281 AC: 1352 AN: 4816

European-Finnish (FIN) AF: 0.0916 AC: 969 AN: 10576

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10714 AN: 67962

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.182 Hom.: 12495

Bravo AF: 0.263

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.45
DANN	Benign	0.78
PhyloP100		-0.15
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: rs16896068; hg19: chr4-17944840;