rs31535

Variant names:

• chr5-135944863-A-G
• rs31535
• ENST00000467490.5:n.1262+2877A>G

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.1262+2877A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,980 control chromosomes in the GnomAD database, including 21,325 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 0.53 (21325 hom., cov: 32)
• Consequence: ENSG00000293402 ENST00000467490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 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+2877A>G		intron_variant	Intron 6 of 6	1
LECT2	ENST00000522943.5	c.289+6360T>C		intron_variant	Intron 3 of 3	3		ENSP00000429618.1
LECT2	ENST00000471827.1	n.393-4183T>C		intron_variant	Intron 2 of 3	5
ENSG00000293402	ENST00000498734.1	n.244+2877A>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80155 AN: 151860 Hom.: 21303 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.528 AC: 80215 AN: 151980 Hom.: 21325 Cov.: 32 AF XY: 0.533 AC XY: 39554 AN XY: 74272

African (AFR) AF: 0.502 AC: 20779 AN: 41420

American (AMR) AF: 0.552 AC: 8430 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2054 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2623 AN: 5170

South Asian (SAS) AF: 0.563 AC: 2711 AN: 4812

European-Finnish (FIN) AF: 0.603 AC: 6377 AN: 10568

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35490 AN: 67952

Other (OTH) AF: 0.500 AC: 1054 AN: 2110

Alfa AF: 0.524 Hom.: 45647

Bravo AF: 0.522

Asia WGS AF: 0.535 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.60
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: rs31535; hg19: chr5-135280552; COSMIC: COSV107282280; COSMIC: COSV107282280;