Genetic Variant ENST00000467490.5:n.386-129G>A (chr5-135940360-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000467490.5(ENSG00000293402):n.386-129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 208,638 control chromosomes in the GnomAD database, including 19,986 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 0.45 ( 15377 hom., cov: 33)

Exomes 𝑓: 0.40 ( 4609 hom. )

Consequence

ENSG00000293402
ENST00000467490.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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.890-129G>A		intron	N/A
	FBXL21P	NR_152421.1		n.894-129G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENSG00000293402	ENST00000467490.5	TSL:1	n.386-129G>A	intron	N/A
ENSG00000293402	ENST00000478939.1	TSL:1	n.290-129G>A	intron	N/A
LECT2	ENST00000522943.5	TSL:3	c.289+10863C>T	intron	N/A	ENSP00000429618.1

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68215

AN:

151758

Hom.:

15361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.532

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.439

Gnomad OTH

AF:

0.445

GnomAD4 exome

AF:

0.396

AC:

22461

AN:

56760

Hom.:

4609

AF XY:

0.398

AC XY:

11540

AN XY:

28968

show subpopulations

African (AFR)

AF:

0.385

AC:

268

AN:

696

American (AMR)

AF:

0.462

AC:

132

AN:

286

Ashkenazi Jewish (ASJ)

AF:

0.411

AC:

226

AN:

550

East Asian (EAS)

AF:

0.471

AC:

209

AN:

444

South Asian (SAS)

AF:

0.456

AC:

1552

AN:

3400

European-Finnish (FIN)

AF:

0.411

AC:

4010

AN:

9752

Middle Eastern (MID)

AF:

0.370

AC:

AN:

138

European-Non Finnish (NFE)

AF:

0.384

AC:

15250

AN:

39674

Other (OTH)

AF:

0.419

AC:

763

AN:

1820

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

678

1357

2035

2714

3392

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.450

AC:

68288

AN:

151878

Hom.:

15377

Cov.:

AF XY:

0.450

AC XY:

33434

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.434

AC:

17978

AN:

41448

American (AMR)

AF:

0.502

AC:

7658

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1653

AN:

3468

East Asian (EAS)

AF:

0.533

AC:

2753

AN:

5166

South Asian (SAS)

AF:

0.493

AC:

2366

AN:

4798

European-Finnish (FIN)

AF:

0.438

AC:

4610

AN:

10522

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.439

AC:

29807

AN:

67910

Other (OTH)

AF:

0.443

AC:

935

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1974

3948

5923

7897

9871

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.440

Hom.:

24944

Bravo

AF:

0.455

Asia WGS

AF:

0.492

AC:

1705

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.5

(source)

DANN

Benign

0.50

PhyloP100

0.014

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