rs925098

Variant names:

• chr4-17918188-G-A
• rs925098
• NM_001394446.1:c.431-8843C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-17918188-G-A
• chr4-17918188-G-C
• chr4-17918188-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.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
• Publications: 24 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 (SAS) allele frequency at 95% confidence interval = 0.824 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.431-8843C>T		intron	N/A	NP_001381375.1
	LCORL	NM_001166139.2		c.431-8843C>T		intron	N/A	NP_001159611.1
	LCORL	NM_001365658.1		c.-50-8843C>T		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.431-8843C>T		intron	N/A	ENSP00000490600.1
	LCORL	ENST00000326877.8	TSL:1	c.431-8843C>T		intron	N/A	ENSP00000317566.3
	LCORL	ENST00000382226.5	TSL:5	c.431-8843C>T		intron	N/A	ENSP00000371661.5

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

African (AFR) AF: 0.655 AC: 27177 AN: 41476

American (AMR) AF: 0.658 AC: 10056 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2785 AN: 5172

South Asian (SAS) AF: 0.846 AC: 4079 AN: 4822

European-Finnish (FIN) AF: 0.681 AC: 7195 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50095 AN: 67990

Other (OTH) AF: 0.695 AC: 1471 AN: 2116

Alfa AF: 0.726 Hom.: 100758

Bravo AF: 0.688

Asia WGS AF: 0.698 AC: 2430 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	7.8
DANN	Benign	0.73
PhyloP100		-0.23
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: rs925098; hg19: chr4-17919811;