5-135924157-T-G

Variant names:

• chr5-135924157-T-G
• rs6861170
• ENST00000522943.5:c.290-1723A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LECT2	ENST00000522943.5	TSL:3	c.290-1723A>C		intron	N/A	ENSP00000429618.1	E5RHW6

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

African (AFR) AF: 0.541 AC: 22391 AN: 41382

American (AMR) AF: 0.310 AC: 4731 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3464

East Asian (EAS) AF: 0.370 AC: 1909 AN: 5156

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4802

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10548

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20653 AN: 67940

Other (OTH) AF: 0.376 AC: 794 AN: 2114

Alfa AF: 0.331 Hom.: 23849

Bravo AF: 0.386

Asia WGS AF: 0.341 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6861170; hg19: chr5-135259846;