rs2516563

Variant names:

• chr5-135946278-G-A
• rs2516563
• ENST00000467490.5:n.1262+4292G>A

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.1262+4292G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,928 control chromosomes in the GnomAD database, including 4,887 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 0.25 (4887 hom., cov: 32)
• Consequence: ENSG00000293402 ENST00000467490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 4 publications found

Genes affected

ENSG00000293402 (HGNC:):

LECT2 (HGNC:6550): (leukocyte cell derived chemotaxin 2) This gene encodes a secreted, 16 kDa protein that acts as a chemotactic factor to neutrophils and stimulates the growth of chondrocytes and osteoblasts. This protein has high sequence similarity to the chondromodulin repeat regions of the chicken myb-induced myeloid 1 protein. A polymorphism in this gene may be associated with rheumatoid arthritis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293402	ENST00000467490.5	n.1262+4292G>A		intron_variant	Intron 6 of 6	1
LECT2	ENST00000522943.5	c.289+4945C>T		intron_variant	Intron 3 of 3	3		ENSP00000429618.1
LECT2	ENST00000471827.1	n.392+4945C>T		intron_variant	Intron 2 of 3	5
ENSG00000293402	ENST00000498734.1	n.244+4292G>A		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38075 AN: 151810 Hom.: 4884 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.251 AC: 38090 AN: 151928 Hom.: 4887 Cov.: 32 AF XY: 0.255 AC XY: 18899 AN XY: 74252

African (AFR) AF: 0.225 AC: 9302 AN: 41422

American (AMR) AF: 0.221 AC: 3370 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1310 AN: 5170

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3316 AN: 10514

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17533 AN: 67950

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.256 Hom.: 2654

Bravo AF: 0.239

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.52
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2516563; hg19: chr5-135281967; COSMIC: COSV50846855; COSMIC: COSV50846855;