rs2516563

Positions:

• chr5-135946278-G-A

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.1262+4292G>A 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 0.251 in 151,928 control chromosomes in the GnomAD database, including 4,887 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 0.25 (4887 hom., cov: 32)
• Consequence: ENST00000467490.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000467490.5	n.1262+4292G>A		intron_variant, non_coding_transcript_variant		1
LECT2	ENST00000522943.5	c.289+4945C>T		intron_variant		3		ENSP00000429618
LECT2	ENST00000471827.1	n.392+4945C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000498734.1	n.244+4292G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38075 AN: 151810 Hom.: 4884 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.251 AC: 38090 AN: 151928 Hom.: 4887 Cov.: 32 AF XY: 0.255 AC XY: 18899 AN XY: 74252

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.241

Alfa AF: 0.255 Hom.: 1635

Bravo AF: 0.239

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2516563; hg19: chr5-135281967; COSMIC: COSV50846855; COSMIC: COSV50846855;