chr4-17982654-T-C

Variant names:

• chr4-17982654-T-C
• rs6840334
• NM_001394446.1:c.155-9769A>G

Variant summary

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

The NM_001394446.1(LCORL):​c.155-9769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,128 control chromosomes in the GnomAD database, including 5,350 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 (5350 hom., cov: 32)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCORL	NM_001394446.1	c.155-9769A>G		intron_variant	Intron 1 of 7	ENST00000635767.2	NP_001381375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCORL	ENST00000635767.2	c.155-9769A>G		intron_variant	Intron 1 of 7	5	NM_001394446.1	ENSP00000490600.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35752 AN: 152010 Hom.: 5317 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.235 AC: 35826 AN: 152128 Hom.: 5350 Cov.: 32 AF XY: 0.231 AC XY: 17206 AN XY: 74386

African (AFR) AF: 0.419 AC: 17398 AN: 41486

American (AMR) AF: 0.193 AC: 2942 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3470

East Asian (EAS) AF: 0.136 AC: 704 AN: 5176

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4822

European-Finnish (FIN) AF: 0.0913 AC: 968 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10731 AN: 67976

Other (OTH) AF: 0.229 AC: 485 AN: 2116

Alfa AF: 0.224 Hom.: 665

Bravo AF: 0.248

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.68
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

Publications

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Other links and lift over

dbSNP: rs6840334; hg19: chr4-17984277;