rs31549

Variant names:

• chr5-135940360-G-A
• rs31549
• ENST00000467490.5:n.386-129G>A

Variant summary

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

The ENST00000522943.5(LECT2):​c.289+10863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 208,638 control chromosomes in the GnomAD database, including 19,986 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 (15377 hom., cov: 33)
  • Exomes 𝑓: 0.40 (4609 hom.)
• Consequence: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• 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]

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522943.5. 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
	FBXL21P	NR_152420.1		n.890-129G>A		intron	N/A
	FBXL21P	NR_152421.1		n.894-129G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.386-129G>A		intron	N/A
	ENSG00000293402	ENST00000478939.1	TSL:1	n.290-129G>A		intron	N/A
	LECT2	ENST00000522943.5	TSL:3	c.289+10863C>T		intron	N/A	ENSP00000429618.1	E5RHW6

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68215 AN: 151758 Hom.: 15361 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.445

GnomAD4 exome AF: 0.396 AC: 22461 AN: 56760 Hom.: 4609 AF XY: 0.398 AC XY: 11540 AN XY: 28968

African (AFR) AF: 0.385 AC: 268 AN: 696

American (AMR) AF: 0.462 AC: 132 AN: 286

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 226 AN: 550

East Asian (EAS) AF: 0.471 AC: 209 AN: 444

South Asian (SAS) AF: 0.456 AC: 1552 AN: 3400

European-Finnish (FIN) AF: 0.411 AC: 4010 AN: 9752

Middle Eastern (MID) AF: 0.370 AC: 51 AN: 138

European-Non Finnish (NFE) AF: 0.384 AC: 15250 AN: 39674

Other (OTH) AF: 0.419 AC: 763 AN: 1820

GnomAD4 genome AF: 0.450 AC: 68288 AN: 151878 Hom.: 15377 Cov.: 33 AF XY: 0.450 AC XY: 33434 AN XY: 74220

African (AFR) AF: 0.434 AC: 17978 AN: 41448

American (AMR) AF: 0.502 AC: 7658 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2753 AN: 5166

South Asian (SAS) AF: 0.493 AC: 2366 AN: 4798

European-Finnish (FIN) AF: 0.438 AC: 4610 AN: 10522

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29807 AN: 67910

Other (OTH) AF: 0.443 AC: 935 AN: 2112

Alfa AF: 0.440 Hom.: 24944

Bravo AF: 0.455

Asia WGS AF: 0.492 AC: 1705 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.50
PhyloP100		0.014
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs31549;

hg19: chr5-135276049;