5-135924157-T-G

Position:

• chr5-135924157-T-G

Variant summary

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

The ENST00000522943.5(LECT2):​c.290-1723A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,860 control chromosomes in the GnomAD database, including 11,620 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 0.38 (11620 hom., cov: 32)
• Consequence: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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
LECT2	ENST00000522943.5	c.290-1723A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56942 AN: 151744 Hom.: 11581 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.379

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.376 AC: 57030 AN: 151860 Hom.: 11620 Cov.: 32 AF XY: 0.374 AC XY: 27791 AN XY: 74212

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.376

Alfa AF: 0.312 Hom.: 12718

Bravo AF: 0.386

Asia WGS AF: 0.341 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6861170; hg19: chr5-135259846;