Genetic Variant NM_002302.3: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:

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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=-0.97).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002302.3. 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
	LECT2	NM_002302.3	MANE Select	c.*390G>A		3_prime_UTR	Exon 4 of 4	NP_002293.2	O14960

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LECT2	ENST00000274507.6	TSL:1 MANE Select	c.*390G>A	3_prime_UTR	Exon 4 of 4	ENSP00000274507.1	O14960
ENSG00000293402	ENST00000467490.5	TSL:1	n.1263-4171C>T	intron	N/A
LECT2	ENST00000522943.5	TSL:3	c.289+4282G>A	intron	N/A	ENSP00000429618.1	E5RHW6

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over