4-17900056-C-T

Variant names:

• chr4-17900056-C-T
• rs979532
• NM_001394446.1:c.682+9038G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394446.1(LCORL):​c.682+9038G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,936 control chromosomes in the GnomAD database, including 41,150 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 0.73 (41150 hom., cov: 31)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCORL	NM_001394446.1	MANE Select	c.682+9038G>A		intron	N/A	NP_001381375.1
	LCORL	NM_001166139.2		c.682+9038G>A		intron	N/A	NP_001159611.1
	LCORL	NM_001365658.1		c.202+9038G>A		intron	N/A	NP_001352587.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCORL	ENST00000635767.2	TSL:5 MANE Select	c.682+9038G>A		intron	N/A	ENSP00000490600.1
	LCORL	ENST00000326877.8	TSL:1	c.682+9038G>A		intron	N/A	ENSP00000317566.3
	LCORL	ENST00000382226.5	TSL:5	c.682+9038G>A		intron	N/A	ENSP00000371661.5

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111328 AN: 151818 Hom.: 41093 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.734 AC: 111448 AN: 151936 Hom.: 41150 Cov.: 31 AF XY: 0.730 AC XY: 54195 AN XY: 74274

African (AFR) AF: 0.759 AC: 31482 AN: 41466

American (AMR) AF: 0.683 AC: 10418 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2638 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2766 AN: 5150

South Asian (SAS) AF: 0.850 AC: 4096 AN: 4820

European-Finnish (FIN) AF: 0.685 AC: 7204 AN: 10520

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50337 AN: 67936

Other (OTH) AF: 0.739 AC: 1561 AN: 2112

Alfa AF: 0.690 Hom.: 3690

Bravo AF: 0.729

Asia WGS AF: 0.705 AC: 2437 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.15
PhyloP100		-0.47
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: rs979532; hg19: chr4-17901679;