dbSNP rs31530: LECT2:c.*390G>A (chr5-135946941-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002302.3(LECT2):c.*390G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 153,616 control chromosomes in the GnomAD database, including 29,556 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 0.62 ( 29236 hom., cov: 31)

Exomes 𝑓: 0.61 ( 320 hom. )

Consequence

LECT2
NM_002302.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.96

Publications

6 publications found

Variant links:

Genes affected

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:

ENSG00000293402 (HGNC:):

ENSG00000293402 links:

Genome browser will be placed here

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=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LECT2	NM_002302.3 link	c.*390G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000274507.6	NP_002293.2	O14960

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LECT2	ENST00000274507.6 link	c.*390G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_002302.3	ENSP00000274507.1		O14960

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

93845

AN:

151804

Hom.:

29212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.592

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.614

AC:

1041

AN:

1696

Hom.:

320

Cov.:

AF XY:

0.612

AC XY:

540

AN XY:

882

show subpopulations

African (AFR)

AF:

0.548

AC:

AN:

American (AMR)

AF:

0.662

AC:

AN:

142

Ashkenazi Jewish (ASJ)

AF:

0.540

AC:

AN:

East Asian (EAS)

AF:

0.552

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.648

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.611

AC:

718

AN:

1176

Other (OTH)

AF:

0.570

AC:

AN:

114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.618

AC:

93904

AN:

151920

Hom.:

29236

Cov.:

AF XY:

0.621

AC XY:

46113

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.570

AC:

23630

AN:

41422

American (AMR)

AF:

0.661

AC:

10100

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.592

AC:

2053

AN:

3470

East Asian (EAS)

AF:

0.643

AC:

3309

AN:

5150

South Asian (SAS)

AF:

0.690

AC:

3320

AN:

4812

European-Finnish (FIN)

AF:

0.660

AC:

6961

AN:

10542

Middle Eastern (MID)

AF:

0.639

AC:

188

AN:

294

European-Non Finnish (NFE)

AF:

0.625

AC:

42441

AN:

67936

Other (OTH)

AF:

0.610

AC:

1287

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1819

3638

5456

7275

9094

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

770

1540

2310

3080

3850

<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:

0.614

Hom.:

7785

Bravo

AF:

0.613

Asia WGS

AF:

0.672

AC:

2334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.12

(source)

DANN

Benign

0.66

PhyloP100

-3.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over