5-135938459-C-T

Variant names:

• chr5-135938459-C-T
• rs31553
• ENST00000467490.5:n.385+912C>T

Variant summary

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

The ENST00000522943.5(LECT2):​c.289+12764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,092 control chromosomes in the GnomAD database, including 45,868 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 0.77 (45863 hom., cov: 30)
  • Exomes 𝑓: 0.64 (5 hom.)
• Consequence: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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.889+912C>T		intron	N/A
	FBXL21P	NR_152421.1		n.893+912C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.385+912C>T		intron	N/A
	ENSG00000293402	ENST00000478939.1	TSL:1	n.289+912C>T		intron	N/A
	LECT2	ENST00000522943.5	TSL:3	c.289+12764G>A		intron	N/A	ENSP00000429618.1	E5RHW6

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116773 AN: 151946 Hom.: 45789 Cov.: 30

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.643 AC: 18 AN: 28 Hom.: 5 AF XY: 0.556 AC XY: 10 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.583 AC: 14 AN: 24

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.769 AC: 116904 AN: 152064 Hom.: 45863 Cov.: 30 AF XY: 0.771 AC XY: 57276 AN XY: 74328

African (AFR) AF: 0.937 AC: 38931 AN: 41534

American (AMR) AF: 0.748 AC: 11415 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2507 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4175 AN: 5160

South Asian (SAS) AF: 0.756 AC: 3634 AN: 4808

European-Finnish (FIN) AF: 0.720 AC: 7602 AN: 10560

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46258 AN: 67948

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.697 Hom.: 37893

Bravo AF: 0.780

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.32
PhyloP100		0.054
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: rs31553; hg19: chr5-135274148;