ENST00000467490.5:n.78+690T>C

Variant names:

• chr5-135931170-T-C
• rs185069
• ENST00000467490.5:n.78+690T>C

Variant summary

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

The ENST00000467490.5(ENSG00000293402):​n.78+690T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,060 control chromosomes in the GnomAD database, including 27,774 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 0.60 (27774 hom., cov: 32)
• Consequence: ENSG00000293402 ENST00000467490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 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+690T>C		intron	N/A
	FBXL21P	NR_152421.1		n.184+690T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293402	ENST00000467490.5	TSL:1	n.78+690T>C		intron	N/A
	LECT2	ENST00000522943.5	TSL:3	c.290-8736A>G		intron	N/A	ENSP00000429618.1
	ENSG00000293402	ENST00000472159.5	TSL:2	n.78+690T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90519 AN: 151942 Hom.: 27765 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.595 AC: 90543 AN: 152060 Hom.: 27774 Cov.: 32 AF XY: 0.599 AC XY: 44553 AN XY: 74350

African (AFR) AF: 0.444 AC: 18402 AN: 41444

American (AMR) AF: 0.653 AC: 9981 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3243 AN: 5160

South Asian (SAS) AF: 0.686 AC: 3306 AN: 4822

European-Finnish (FIN) AF: 0.699 AC: 7402 AN: 10596

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44359 AN: 67968

Other (OTH) AF: 0.592 AC: 1247 AN: 2108

Alfa AF: 0.626 Hom.: 38638

Bravo AF: 0.583

Asia WGS AF: 0.653 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		-0.61
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: rs185069; hg19: chr5-135266859; COSMIC: COSV71929989;