3-156978717-A-G

Variant names:

• chr3-156978717-A-G
• rs10936043
• NM_001004316.3:c.746-477A>G

Variant summary

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

The NM_001004316.3(LEKR1):​c.746-477A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,814 control chromosomes in the GnomAD database, including 16,052 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 0.43 (16052 hom., cov: 31)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LEKR1	NM_001004316.3	c.746-477A>G		intron_variant	Intron 6 of 12	ENST00000356539.9	NP_001004316.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEKR1	ENST00000356539.9	c.746-477A>G		intron_variant	Intron 6 of 12	5	NM_001004316.3	ENSP00000348936.4
LEKR1	ENST00000470811.6	n.746-477A>G		intron_variant	Intron 6 of 13	2		ENSP00000418214.2
LEKR1	ENST00000489350.5	n.447-477A>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64786 AN: 151696 Hom.: 16052 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.427 AC: 64778 AN: 151814 Hom.: 16052 Cov.: 31 AF XY: 0.432 AC XY: 32008 AN XY: 74160

African (AFR) AF: 0.165 AC: 6842 AN: 41412

American (AMR) AF: 0.581 AC: 8852 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1896 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3746 AN: 5160

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4816

European-Finnish (FIN) AF: 0.465 AC: 4872 AN: 10472

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34559 AN: 67938

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.499 Hom.: 32694

Bravo AF: 0.427

Asia WGS AF: 0.565 AC: 1964 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	9.0
DANN	Benign	0.81
PhyloP100		0.098
Mutation Taster		=99/1	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: rs10936043; hg19: chr3-156696506;