dbSNP rs31549: ENSG00000293402: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXL21P	NR_152420.1 link	n.890-129G>A		intron_variant	Intron 5 of 5
FBXL21P	NR_152421.1 link	n.894-129G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000293402	ENST00000467490.5 link	n.386-129G>A	intron_variant	Intron 4 of 6	1
ENSG00000293402	ENST00000478939.1 link	n.290-129G>A	intron_variant	Intron 2 of 2	1
LECT2	ENST00000522943.5 link	c.289+10863C>T	intron_variant	Intron 3 of 3	3	ENSP00000429618.1	E5RHW6

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

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

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 v4.3

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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rs31549

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over