NM_001004316.3:c.48+8818T>C

Variant names:

• chr3-156838195-T-C
• rs344081
• NM_001004316.3:c.48+8818T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 36 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	NM_001004316.3	MANE Select	c.48+8818T>C		intron	N/A	NP_001004316.2	J3KP02
	LEKR1	NM_001193283.2		c.48+8818T>C		intron	N/A	NP_001180212.1	Q6ZMV7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LEKR1	ENST00000356539.9	TSL:5 MANE Select	c.48+8818T>C		intron	N/A	ENSP00000348936.4	J3KP02
	LEKR1	ENST00000491763.1	TSL:1	c.48+8818T>C		intron	N/A	ENSP00000474182.1	Q6ZMV7
	LEKR1	ENST00000477399.5	TSL:2	c.48+8818T>C		intron	N/A	ENSP00000425282.1	Q6ZMV7

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

African (AFR) AF: 0.504 AC: 20854 AN: 41400

American (AMR) AF: 0.112 AC: 1706 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3468

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5172

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10580

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8949 AN: 67994

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.159 Hom.: 10944

Bravo AF: 0.238

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.87
PhyloP100		0.30
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: rs344081; hg19: chr3-156555984;