rs344081

Positions:

• chr3-156838195-T-C

Variant summary

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

The NM_001004316.3(LEKR1):​c.48+8818T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,040 control chromosomes in the GnomAD database, including 6,438 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 0.24 (6438 hom., cov: 32)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LEKR1	NM_001004316.3	c.48+8818T>C		intron_variant		ENST00000356539.9
LEKR1	NM_001193283.2	c.48+8818T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LEKR1	ENST00000356539.9	c.48+8818T>C		intron_variant		5	NM_001004316.3	P1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35891 AN: 151922 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.236 AC: 35949 AN: 152040 Hom.: 6438 Cov.: 32 AF XY: 0.236 AC XY: 17522 AN XY: 74318

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.215

Alfa AF: 0.139 Hom.: 3125

Bravo AF: 0.238

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.87

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: rs344081; hg19: chr3-156555984;