rs17701996

Variant names:

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

Variant summary

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

The ENST00000522943.5(LECT2):​c.290-9214T>C 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: LECT2 ENST00000522943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

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]

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXL21P	NR_152420.1	n.184+1168A>G		intron_variant	Intron 1 of 5
FBXL21P	NR_152421.1	n.184+1168A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXL21P	ENST00000467490.5	n.78+1168A>G		intron_variant	Intron 1 of 6	1
LECT2	ENST00000522943.5	c.290-9214T>C		intron_variant	Intron 3 of 3	3		ENSP00000429618.1
FBXL21P	ENST00000472159.5	n.78+1168A>G		intron_variant	Intron 1 of 4	2

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

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.0589

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0916

Gnomad4 NFE AF: 0.0733

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.0715 Hom.: 528

Bravo AF: 0.0688

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17701996; hg19: chr5-135267337;