chr3-156908302-C-T

Variant names:

• chr3-156908302-C-T
• rs12638253
• NM_001004316.3:c.264-12273C>T

Variant summary

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

The NM_001004316.3(LEKR1):​c.264-12273C>T 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 151,894 control chromosomes in the GnomAD database, including 16,063 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 (16063 hom., cov: 31)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 23 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=-0.95).
• 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.264-12273C>T		intron_variant	Intron 3 of 12	ENST00000356539.9	NP_001004316.2
LEKR1	NM_001193283.2	c.264-12273C>T		intron_variant	Intron 3 of 4		NP_001180212.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEKR1	ENST00000356539.9	c.264-12273C>T		intron_variant	Intron 3 of 12	5	NM_001004316.3	ENSP00000348936.4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64808 AN: 151776 Hom.: 16063 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.488

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: 64800 AN: 151894 Hom.: 16063 Cov.: 31 AF XY: 0.432 AC XY: 32036 AN XY: 74236

African (AFR) AF: 0.165 AC: 6847 AN: 41464

American (AMR) AF: 0.582 AC: 8873 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3750 AN: 5160

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.465 AC: 4897 AN: 10526

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

European-Non Finnish (NFE) AF: 0.509 AC: 34530 AN: 67882

Other (OTH) AF: 0.474 AC: 1003 AN: 2114

Alfa AF: 0.495 Hom.: 65408

Bravo AF: 0.427

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.57
PhyloP100		-0.93
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: rs12638253; hg19: chr3-156626091;