3-157010821-G-A

Variant names:

• chr3-157010821-G-A
• rs7616559
• NM_001004316.3:c.1110-592G>A

Variant summary

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

The NM_001004316.3(LEKR1):​c.1110-592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,932 control chromosomes in the GnomAD database, including 40,885 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 (40885 hom., cov: 32)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 12 publications found

Genes affected

LEKR1 (HGNC:33765): (leucine, glutamate and lysine rich 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004316.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	NM_001004316.3	MANE Select	c.1110-592G>A		intron	N/A	NP_001004316.2	J3KP02

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	ENST00000356539.9	TSL:5 MANE Select	c.1110-592G>A		intron	N/A	ENSP00000348936.4	J3KP02
	LEKR1	ENST00000470811.6	TSL:2	n.*588-592G>A		intron	N/A	ENSP00000418214.2	A0A8I5FW65

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110692 AN: 151814 Hom.: 40850 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.729 AC: 110778 AN: 151932 Hom.: 40885 Cov.: 32 AF XY: 0.737 AC XY: 54772 AN XY: 74270

African (AFR) AF: 0.633 AC: 26225 AN: 41444

American (AMR) AF: 0.808 AC: 12335 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3470

East Asian (EAS) AF: 0.935 AC: 4828 AN: 5166

South Asian (SAS) AF: 0.921 AC: 4447 AN: 4826

European-Finnish (FIN) AF: 0.741 AC: 7823 AN: 10564

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50016 AN: 67878

Other (OTH) AF: 0.744 AC: 1570 AN: 2110

Alfa AF: 0.737 Hom.: 68975

Bravo AF: 0.727

Asia WGS AF: 0.911 AC: 3167 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.47
PhyloP100		-0.57
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: rs7616559; hg19: chr3-156728610;