3-156855425-A-G

Variant names:

• chr3-156855425-A-G
• rs2633815
• NM_001004316.3:c.263+2443A>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.263+2443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,952 control chromosomes in the GnomAD database, including 9,979 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 0.30 (9979 hom., cov: 32)
• Consequence: LEKR1 NM_001004316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	NM_001004316.3	MANE Select	c.263+2443A>G		intron	N/A	NP_001004316.2
	LEKR1	NM_001193283.2		c.263+2443A>G		intron	N/A	NP_001180212.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	ENST00000356539.9	TSL:5 MANE Select	c.263+2443A>G		intron	N/A	ENSP00000348936.4
	LEKR1	ENST00000491763.1	TSL:1	c.263+2443A>G		intron	N/A	ENSP00000474182.1
	LEKR1	ENST00000477399.5	TSL:2	c.263+2443A>G		intron	N/A	ENSP00000425282.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46058 AN: 151834 Hom.: 9936 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.304 AC: 46155 AN: 151952 Hom.: 9979 Cov.: 32 AF XY: 0.302 AC XY: 22419 AN XY: 74280

African (AFR) AF: 0.615 AC: 25460 AN: 41410

American (AMR) AF: 0.185 AC: 2826 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3464

East Asian (EAS) AF: 0.0369 AC: 191 AN: 5178

South Asian (SAS) AF: 0.264 AC: 1273 AN: 4814

European-Finnish (FIN) AF: 0.223 AC: 2353 AN: 10570

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12413 AN: 67914

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.260 Hom.: 853

Bravo AF: 0.312

Asia WGS AF: 0.196 AC: 680 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.71
PhyloP100		-0.40
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: rs2633815; hg19: chr3-156573214;