rs31530

Variant names:

• chr5-135946941-C-T
• rs31530
• NM_002302.3:c.*390G>A

Variant summary

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

The NM_002302.3(LECT2):​c.*390G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 153,616 control chromosomes in the GnomAD database, including 29,556 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 0.62 (29236 hom., cov: 31)
  • Exomes 𝑓: 0.61 (320 hom.)
• Consequence: LECT2 NM_002302.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

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]

FBXL21P (HGNC:13600): (F-box and leucine rich repeat protein 21, pseudogene) This locus represents a transcribed pseudogene that is related to genes encoding members of the F-box family of proteins. [provided by RefSeq, Nov 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LECT2	NM_002302.3	c.*390G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000274507.6	NP_002293.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LECT2	ENST00000274507	c.*390G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_002302.3	ENSP00000274507.1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93845 AN: 151804 Hom.: 29212 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.614 AC: 1041 AN: 1696 Hom.: 320 Cov.: 0 AF XY: 0.612 AC XY: 540 AN XY: 882

Gnomad4 AFR exome AF: 0.548

Gnomad4 AMR exome AF: 0.662

Gnomad4 ASJ exome AF: 0.540

Gnomad4 EAS exome AF: 0.552

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.648

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 0.570

GnomAD4 genome AF: 0.618 AC: 93904 AN: 151920 Hom.: 29236 Cov.: 31 AF XY: 0.621 AC XY: 46113 AN XY: 74250

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.610

Alfa AF: 0.615 Hom.: 3624

Bravo AF: 0.613

Asia WGS AF: 0.672 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.66

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: rs31530; hg19: chr5-135282630; COSMIC: COSV50846858; COSMIC: COSV50846858;