Variant chr5-135951340-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002302.3(LECT2):c.172A>G(p.Ile58Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,612,554 control chromosomes in the GnomAD database, including 320,989 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.62 ( 29324 hom., cov: 32)

Exomes 𝑓: 0.63 ( 291665 hom. )

Consequence

LECT2
NM_002302.3 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.496

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0176246E-6).

BP6

Variant 5-135951340-T-C is Benign according to our data. Variant chr5-135951340-T-C is described in ClinVar as [Benign]. Clinvar id is 3060729.Status of the report is no_assertion_criteria_provided, 0 stars.

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/exons	MANE	Protein	UniProt
LECT2	NM_002302.3 linkuse as main transcript	c.172A>G	p.Ile58Val	missense_variant	3/4	ENST00000274507.6	NP_002293.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LECT2	ENST00000274507.6 linkuse as main transcript	c.172A>G	p.Ile58Val	missense_variant	3/4	1	NM_002302.3	ENSP00000274507	P1
	ENST00000467490.5 linkuse as main transcript	n.1491T>C		non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes

AF:

0.619

AC:

94004

AN:

151920

Hom.:

29301

Cov.:

show subpopulations

Gnomad AFR

AF:

0.573

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.592

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.607

GnomAD3 exomes

AF:

0.645

AC:

161816

AN:

251034

Hom.:

52372

AF XY:

0.645

AC XY:

87525

AN XY:

135636

show subpopulations

Gnomad AFR exome

AF:

0.569

Gnomad AMR exome

AF:

0.701

Gnomad ASJ exome

AF:

0.590

Gnomad EAS exome

AF:

0.645

Gnomad SAS exome

AF:

0.676

Gnomad FIN exome

AF:

0.665

Gnomad NFE exome

AF:

0.632

Gnomad OTH exome

AF:

0.625

GnomAD4 exome

AF:

0.631

AC:

921347

AN:

1460516

Hom.:

291665

Cov.:

AF XY:

0.632

AC XY:

459492

AN XY:

726604

show subpopulations

Gnomad4 AFR exome

AF:

0.565

Gnomad4 AMR exome

AF:

0.694

Gnomad4 ASJ exome

AF:

0.587

Gnomad4 EAS exome

AF:

0.610

Gnomad4 SAS exome

AF:

0.678

Gnomad4 FIN exome

AF:

0.662

Gnomad4 NFE exome

AF:

0.627

Gnomad4 OTH exome

AF:

0.624

GnomAD4 genome

AF:

0.619

AC:

94062

AN:

152038

Hom.:

29324

Cov.:

AF XY:

0.622

AC XY:

46185

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.573

Gnomad4 AMR

AF:

0.661

Gnomad4 ASJ

AF:

0.592

Gnomad4 EAS

AF:

0.641

Gnomad4 SAS

AF:

0.689

Gnomad4 FIN

AF:

0.660

Gnomad4 NFE

AF:

0.625

Gnomad4 OTH

AF:

0.611

Alfa

AF:

0.624

Hom.:

75811

Bravo

AF:

0.614

TwinsUK

AF:

0.610

AC:

2261

ALSPAC

AF:

0.630

AC:

2429

ESP6500AA

AF:

0.579

AC:

2550

ESP6500EA

AF:

0.636

AC:

5472

ExAC

AF:

0.644

AC:

78237

Asia WGS

AF:

0.673

AC:

2338

AN:

3478

EpiCase

AF:

0.628

EpiControl

AF:

0.636

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

LECT2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

5.6

DANN

Benign

0.62

DEOGEN2

Benign

0.019

T;T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.50

T;T;T

MetaRNN

Benign

0.0000010

T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

-1.1

.;N;.

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.11

N;N;N

REVEL

Benign

0.14

Sift

Benign

0.53

T;T;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0

.;B;.

Vest4

0.025

MPC

0.023

ClinPred

0.0013

GERP RS

3.3

Varity_R

0.023

gMVP

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over