4-17852432-T-G

Position:

• chr4-17852432-T-G

Variant summary

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

The NM_001394446.1(LCORL):​c.5603-6531A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 151,964 control chromosomes in the GnomAD database, including 41,068 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 (41068 hom., cov: 32)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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]

LCORL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCORL	NM_001394446.1	c.5603-6531A>C		intron_variant		ENST00000635767.2	NP_001381375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCORL	ENST00000635767.2	c.5603-6531A>C		intron_variant		5	NM_001394446.1	ENSP00000490600.1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111267 AN: 151848 Hom.: 41020 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.733 AC: 111375 AN: 151964 Hom.: 41068 Cov.: 32 AF XY: 0.731 AC XY: 54269 AN XY: 74278

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.747

Alfa AF: 0.739 Hom.: 52652

Bravo AF: 0.725

Asia WGS AF: 0.712 AC: 2480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6842303; hg19: chr4-17854055;