rs17701996

Variant names:

• chr5-135931648-A-G
• rs17701996
• ENST00000467490.5:n.78+1168A>G

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.78+1168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,302 control chromosomes in the GnomAD database, including 452 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 0.072 (452 hom., cov: 33)
• Consequence: ENSG00000293402 ENST00000467490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467490.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL21P	NR_152420.1		n.184+1168A>G		intron	N/A
	FBXL21P	NR_152421.1		n.184+1168A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.78+1168A>G		intron	N/A
	LECT2	ENST00000522943.5	TSL:3	c.290-9214T>C		intron	N/A	ENSP00000429618.1
	ENSG00000293402	ENST00000472159.5	TSL:2	n.78+1168A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10893 AN: 152184 Hom.: 451 Cov.: 33

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0716 AC: 10904 AN: 152302 Hom.: 452 Cov.: 33 AF XY: 0.0733 AC XY: 5457 AN XY: 74476

African (AFR) AF: 0.0495 AC: 2059 AN: 41578

American (AMR) AF: 0.0589 AC: 902 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3472

East Asian (EAS) AF: 0.142 AC: 736 AN: 5170

South Asian (SAS) AF: 0.116 AC: 558 AN: 4830

European-Finnish (FIN) AF: 0.0916 AC: 971 AN: 10606

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0733 AC: 4985 AN: 68026

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.0710 Hom.: 670

Bravo AF: 0.0688

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.7
DANN	Benign	0.79
PhyloP100		1.2
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: rs17701996; hg19: chr5-135267337;