Genetic Variant NM_002302.3:c.289+475T>C (chr5-135950748-A-G) – 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.289+475T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 162,388 control chromosomes in the GnomAD database, including 16,453 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 ( 15445 hom., cov: 33)

Exomes 𝑓: 0.43 ( 1008 hom. )

Consequence

LECT2
NM_002302.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.499

Publications

7 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=-0.68).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.481 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LECT2	NM_002302.3	MANE Select	c.289+475T>C		intron	N/A	NP_002293.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LECT2	ENST00000274507.6	TSL:1 MANE Select	c.289+475T>C	intron	N/A	ENSP00000274507.1
ENSG00000293402	ENST00000467490.5	TSL:1	n.1263-364A>G	intron	N/A
LECT2	ENST00000522943.5	TSL:3	c.289+475T>C	intron	N/A	ENSP00000429618.1

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68079

AN:

151934

Hom.:

15431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.493

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.365

Gnomad SAS

AF:

0.450

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.432

AC:

4466

AN:

10336

Hom.:

1008

Cov.:

AF XY:

0.415

AC XY:

2159

AN XY:

5200

show subpopulations

African (AFR)

AF:

0.412

AC:

186

AN:

452

American (AMR)

AF:

0.462

AC:

171

AN:

370

Ashkenazi Jewish (ASJ)

AF:

0.404

AC:

169

AN:

418

East Asian (EAS)

AF:

0.365

AC:

146

AN:

400

South Asian (SAS)

AF:

0.366

AC:

AN:

112

European-Finnish (FIN)

AF:

0.515

AC:

207

AN:

402

Middle Eastern (MID)

AF:

0.453

AC:

AN:

European-Non Finnish (NFE)

AF:

0.434

AC:

3223

AN:

7424

Other (OTH)

AF:

0.424

AC:

294

AN:

694

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

120

240

359

479

599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<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:

0.448

AC:

68121

AN:

152052

Hom.:

15445

Cov.:

AF XY:

0.451

AC XY:

33520

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.422

AC:

17481

AN:

41444

American (AMR)

AF:

0.490

AC:

7490

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.457

AC:

1585

AN:

3468

East Asian (EAS)

AF:

0.365

AC:

1884

AN:

5168

South Asian (SAS)

AF:

0.447

AC:

2155

AN:

4816

European-Finnish (FIN)

AF:

0.512

AC:

5405

AN:

10554

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.450

AC:

30626

AN:

67994

Other (OTH)

AF:

0.428

AC:

905

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1955

3910

5864

7819

9774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.448

Hom.:

61451

Bravo

AF:

0.444

Asia WGS

AF:

0.424

AC:

1473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

7.0

(source)

DANN

Benign

0.89

PhyloP100

-0.50

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