rs31535

Variant names:

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

Variant summary

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

The ENST00000522943.5(LECT2):​c.289+6360T>C 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: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

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]

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

Verdict is Benign. Variant got -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
FBXL21P	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
FBXL21P	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

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.500

Alfa AF: 0.523 Hom.: 27643

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31535; hg19: chr5-135280552;