3-157038871-A-G

Position:

• chr3-157038871-A-G

Variant summary

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

The NM_001004316.3(LEKR1):​c.1669-6469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,116 control chromosomes in the GnomAD database, including 39,790 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 0.72 (39790 hom., cov: 32)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LEKR1	NM_001004316.3	c.1669-6469A>G		intron_variant		ENST00000356539.9	NP_001004316.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LEKR1	ENST00000356539.9	c.1669-6469A>G		intron_variant		5	NM_001004316.3	ENSP00000348936.4
LEKR1	ENST00000470811.6	n.*1147-6469A>G		intron_variant		2		ENSP00000418214.2

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109245 AN: 151998 Hom.: 39756 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.719 AC: 109331 AN: 152116 Hom.: 39790 Cov.: 32 AF XY: 0.727 AC XY: 54085 AN XY: 74356

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.731

Alfa AF: 0.715 Hom.: 13494

Bravo AF: 0.719

Asia WGS AF: 0.911 AC: 3168 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	1.0
DANN	Benign	0.55

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

LitVar

Other links and lift over

dbSNP: rs1384542; hg19: chr3-156756660;