rs17169429

Variant names:

• chr5-135936789-A-G
• rs17169429
• ENST00000467490.5:n.106-15A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000467490.5(ENSG00000293402):​n.106-15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,367,592 control chromosomes in the GnomAD database, including 290 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 0.030 (163 hom., cov: 32)
  • Exomes 𝑓: 0.0080 (127 hom.)
• Consequence: ENSG00000293402 ENST00000467490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 4 publications found

Genes affected

ENSG00000293402 (HGNC:):

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 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.595A>G		non_coding_transcript_exon	Exon 4 of 6
	FBXL21P	NR_152421.1		n.599A>G		non_coding_transcript_exon	Exon 4 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.106-15A>G		intron	N/A
	FBXL21P	ENST00000297158.11	TSL:6	n.277A>G		non_coding_transcript_exon	Exon 2 of 5
	ENSG00000293402	ENST00000475169.1	TSL:2	n.560A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4577 AN: 152122 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00733

Gnomad OTH AF: 0.0292

GnomAD2 exomes AF: 0.0123 AC: 3054 AN: 249140 AF XY: 0.0106

Gnomad AFR exome AF: 0.0839

Gnomad AMR exome AF: 0.0107

Gnomad ASJ exome AF: 0.00954

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0157

Gnomad NFE exome AF: 0.00746

Gnomad OTH exome AF: 0.0114

GnomAD4 exome AF: 0.00804 AC: 9768 AN: 1215352 Hom.: 127 Cov.: 31 AF XY: 0.00759 AC XY: 4574 AN XY: 602312

African (AFR) AF: 0.0857 AC: 2252 AN: 26292

American (AMR) AF: 0.0112 AC: 419 AN: 37290

Ashkenazi Jewish (ASJ) AF: 0.00965 AC: 163 AN: 16894

East Asian (EAS) AF: 0.00 AC: 0 AN: 16806

South Asian (SAS) AF: 0.00127 AC: 106 AN: 83216

European-Finnish (FIN) AF: 0.0148 AC: 482 AN: 32574

Middle Eastern (MID) AF: 0.0342 AC: 153 AN: 4474

European-Non Finnish (NFE) AF: 0.00600 AC: 5720 AN: 953806

Other (OTH) AF: 0.0107 AC: 473 AN: 44000

GnomAD4 genome AF: 0.0302 AC: 4592 AN: 152240 Hom.: 163 Cov.: 32 AF XY: 0.0295 AC XY: 2193 AN XY: 74426

African (AFR) AF: 0.0848 AC: 3522 AN: 41516

American (AMR) AF: 0.0182 AC: 279 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4816

European-Finnish (FIN) AF: 0.0155 AC: 164 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00734 AC: 499 AN: 68026

Other (OTH) AF: 0.0289 AC: 61 AN: 2114

Alfa AF: 0.0182 Hom.: 58

Bravo AF: 0.0334

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	0.17
DANN	Benign	0.75
PhyloP100		-0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs17169429; hg19: chr5-135272478;