dbSNP rs17169429: ENSG00000293402:n.106-15A>G (chr5-135936789-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000522943.5(LECT2):c.290-14355T>C 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

LECT2
ENST00000522943.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477

Publications

4 publications found

Variant links:

Genes affected

ENSG00000293402 (HGNC:):

ENSG00000293402 links:

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]

LECT2 links:

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]

FBXL21P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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: ENST00000522943.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000293402	ENST00000467490.5	TSL:1	n.106-15A>G	intron	N/A
LECT2	ENST00000522943.5	TSL:3	c.290-14355T>C	intron	N/A	ENSP00000429618.1	E5RHW6
FBXL21P	ENST00000297158.11	TSL:6	n.277A>G	non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.0301

AC:

4577

AN:

152122

Hom.:

162

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.00759

AC XY:

4574

AN XY:

602312

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

454

908

1362

1816

2270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

286

572

858

1144

1430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0302

AC:

4592

AN:

152240

Hom.:

163

Cov.:

AF XY:

0.0295

AC XY:

2193

AN XY:

74426

show subpopulations

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:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00166

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.0155

AC:

164

AN:

10614

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00734

AC:

499

AN:

68026

Other (OTH)

AF:

0.0289

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

220

439

659

878

1098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0182

Hom.:

Bravo

AF:

0.0334

Asia WGS

AF:

0.00751

AC:

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

(source)

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)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over