Variant rs31519 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

FBXL21P (HGNC:):

FBXL21P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LECT2	NM_002302.3 linkuse as main transcript	c.289+475T>C		intron_variant		ENST00000274507.6	NP_002293.2	O14960

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LECT2	ENST00000274507.6 linkuse as main transcript	c.289+475T>C		intron_variant		1	NM_002302.3	ENSP00000274507.1		O14960

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

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.462

Gnomad4 ASJ exome

AF:

0.404

Gnomad4 EAS exome

AF:

0.365

Gnomad4 SAS exome

AF:

0.366

Gnomad4 FIN exome

AF:

0.515

Gnomad4 NFE exome

AF:

0.434

Gnomad4 OTH exome

AF:

0.424

GnomAD4 genome

AF:

0.448

AC:

68121

AN:

152052

Hom.:

15445

Cov.:

AF XY:

0.451

AC XY:

33520

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.422

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.365

Gnomad4 SAS

AF:

0.447

Gnomad4 FIN

AF:

0.512

Gnomad4 NFE

AF:

0.450

Gnomad4 OTH

AF:

0.428

Alfa

AF:

0.448

Hom.:

26186

Bravo

AF:

0.444

Asia WGS

AF:

0.424

AC:

1473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

7.0

DANN

Benign

0.89

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over