rs16896210

Variant names:

• chr4-17990709-A-G
• rs16896210
• NM_001394446.1:c.155-17824T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-17990709-A-G
• chr4-17990709-A-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.155-17824T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 149,120 control chromosomes in the GnomAD database, including 5,834 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 (5834 hom., cov: 28)
• Consequence: LCORL NM_001394446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCORL	NM_001394446.1	c.155-17824T>C		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.155-17824T>C		intron_variant	Intron 1 of 7	5	NM_001394446.1	ENSP00000490600.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 36502 AN: 149022 Hom.: 5805 Cov.: 28

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.245 AC: 36570 AN: 149120 Hom.: 5834 Cov.: 28 AF XY: 0.242 AC XY: 17538 AN XY: 72476

African (AFR) AF: 0.454 AC: 18234 AN: 40196

American (AMR) AF: 0.200 AC: 2984 AN: 14910

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 973 AN: 3452

East Asian (EAS) AF: 0.138 AC: 696 AN: 5058

South Asian (SAS) AF: 0.278 AC: 1302 AN: 4684

European-Finnish (FIN) AF: 0.0921 AC: 911 AN: 9892

Middle Eastern (MID) AF: 0.205 AC: 59 AN: 288

European-Non Finnish (NFE) AF: 0.158 AC: 10696 AN: 67658

Other (OTH) AF: 0.239 AC: 496 AN: 2078

Alfa AF: 0.208 Hom.: 6182

Bravo AF: 0.260

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.67
PhyloP100		-1.1
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: rs16896210; hg19: chr4-17992332;