rs31535

Positions:

• chr5-135944863-A-G

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.1262+2877A>G variant causes a intron, non coding transcript 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: ENST00000467490.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

(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

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000467490.5	n.1262+2877A>G		intron_variant, non_coding_transcript_variant		1
LECT2	ENST00000522943.5	c.289+6360T>C		intron_variant		3
LECT2	ENST00000471827.1	n.393-4183T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000498734.1	n.244+2877A>G		intron_variant, non_coding_transcript_variant		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;