rs31555

Variant names:

• chr5-135935932-A-C
• rs31555
• ENST00000467490.5:n.106-872A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-135935932-A-C
• chr5-135935932-A-G

Variant summary

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

The ENST00000522943.5(LECT2):​c.290-13498T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,044 control chromosomes in the GnomAD database, including 7,394 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 0.30 (7394 hom., cov: 32)
• Consequence: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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.399+493A>C		intron	N/A
	FBXL21P	NR_152421.1		n.403+493A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.106-872A>C		intron	N/A
	LECT2	ENST00000522943.5	TSL:3	c.290-13498T>G		intron	N/A	ENSP00000429618.1	E5RHW6
	FBXL21P	ENST00000297158.11	TSL:6	n.83-663A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45869 AN: 151926 Hom.: 7394 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.302 AC: 45882 AN: 152044 Hom.: 7394 Cov.: 32 AF XY: 0.302 AC XY: 22408 AN XY: 74318

African (AFR) AF: 0.189 AC: 7846 AN: 41510

American (AMR) AF: 0.397 AC: 6060 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.374 AC: 1932 AN: 5172

South Asian (SAS) AF: 0.362 AC: 1748 AN: 4824

European-Finnish (FIN) AF: 0.300 AC: 3162 AN: 10546

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23324 AN: 67966

Other (OTH) AF: 0.309 AC: 651 AN: 2106

Alfa AF: 0.313 Hom.: 1231

Bravo AF: 0.304

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs31555;

hg19: chr5-135271621;