rs31519

chr5-135950748-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002302.3(LECT2):c.289+475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 162,388 control chromosomes in the GnomAD database, including 16,453 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 0.45 (15445 hom., cov: 33)
  • Exomes 𝑓: 0.43 (1008 hom.)
• Consequence: LECT2 NM_002302.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LECT2	NM_002302.3	c.289+475T>C		intron_variant		ENST00000274507.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LECT2	ENST00000274507.6	c.289+475T>C		intron_variant		1	NM_002302.3	P1
	ENST00000467490.5	n.1263-364A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68079 AN: 151934 Hom.: 15431 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.425

GnomAD4 exome AF: 0.432 AC: 4466 AN: 10336 Hom.: 1008 Cov.: 0 AF XY: 0.415 AC XY: 2159 AN XY: 5200

Gnomad4 AFR exome AF: 0.412

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.404

Gnomad4 EAS exome AF: 0.365

Gnomad4 SAS exome AF: 0.366

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.434

Gnomad4 OTH exome AF: 0.424

GnomAD4 genome AF: 0.448 AC: 68121 AN: 152052 Hom.: 15445 Cov.: 33 AF XY: 0.451 AC XY: 33520 AN XY: 74298

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.428

Alfa AF: 0.448 Hom.: 26186

Bravo AF: 0.444

Asia WGS AF: 0.424 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	7.0
Dann	Benign	0.89

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

Publications

LitVar

Other links and lift over

dbSNP: rs31519; hg19: chr5-135286437; COSMIC: COSV50846880; COSMIC: COSV50846880;