Variant 14-55145121-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002306.4(LGALS3):c.603A>T(p.Gln201His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 1,612,430 control chromosomes in the GnomAD database, including 4,848 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 0.057 ( 310 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4538 hom. )

Consequence

LGALS3
NM_002306.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.213

Variant links:

Genes affected

LGALS3 (HGNC:6563): (galectin 3) This gene encodes a member of the galectin family of carbohydrate binding proteins. Members of this protein family have an affinity for beta-galactosides. The encoded protein is characterized by an N-terminal proline-rich tandem repeat domain and a single C-terminal carbohydrate recognition domain. This protein can self-associate through the N-terminal domain allowing it to bind to multivalent saccharide ligands. This protein localizes to the extracellular matrix, the cytoplasm and the nucleus. This protein plays a role in numerous cellular functions including apoptosis, innate immunity, cell adhesion and T-cell regulation. The protein exhibits antimicrobial activity against bacteria and fungi. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2014]

LGALS3 links:

LGALS3 (HGNC:):

LGALS3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023002028).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS3	NM_002306.4 linkuse as main transcript	c.603A>T	p.Gln201His	missense_variant	6/6	ENST00000254301.14	NP_002297.2	P17931A0A024R693
LGALS3	NM_001357678.2 linkuse as main transcript	c.645A>T	p.Gln215His	missense_variant	7/7		NP_001344607.1
LGALS3	NR_003225.2 linkuse as main transcript	n.1647A>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS3	ENST00000254301.14 linkuse as main transcript	c.603A>T	p.Gln201His	missense_variant	6/6	1	NM_002306.4	ENSP00000254301.9		P17931
LGALS3	ENST00000556438.6 linkuse as main transcript	n.1442A>T		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes

AF:

0.0572

AC:

8699

AN:

152152

Hom.:

310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0137

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.0641

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.0899

Gnomad FIN

AF:

0.0741

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0796

Gnomad OTH

AF:

0.0626

GnomAD3 exomes

AF:

0.0651

AC:

16210

AN:

248824

Hom.:

661

AF XY:

0.0685

AC XY:

9248

AN XY:

135014

show subpopulations

Gnomad AFR exome

AF:

0.0130

Gnomad AMR exome

AF:

0.0415

Gnomad ASJ exome

AF:

0.0629

Gnomad EAS exome

AF:

0.00167

Gnomad SAS exome

AF:

0.0939

Gnomad FIN exome

AF:

0.0732

Gnomad NFE exome

AF:

0.0803

Gnomad OTH exome

AF:

0.0692

GnomAD4 exome

AF:

0.0758

AC:

110683

AN:

1460160

Hom.:

4538

Cov.:

AF XY:

0.0764

AC XY:

55505

AN XY:

726504

show subpopulations

Gnomad4 AFR exome

AF:

0.0119

Gnomad4 AMR exome

AF:

0.0436

Gnomad4 ASJ exome

AF:

0.0615

Gnomad4 EAS exome

AF:

0.00116

Gnomad4 SAS exome

AF:

0.0953

Gnomad4 FIN exome

AF:

0.0752

Gnomad4 NFE exome

AF:

0.0810

Gnomad4 OTH exome

AF:

0.0683

GnomAD4 genome

AF:

0.0571

AC:

8701

AN:

152270

Hom.:

310

Cov.:

AF XY:

0.0570

AC XY:

4244

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0137

Gnomad4 AMR

AF:

0.0640

Gnomad4 ASJ

AF:

0.0600

Gnomad4 EAS

AF:

0.00386

Gnomad4 SAS

AF:

0.0906

Gnomad4 FIN

AF:

0.0741

Gnomad4 NFE

AF:

0.0797

Gnomad4 OTH

AF:

0.0620

Alfa

AF:

0.0687

Hom.:

293

Bravo

AF:

0.0533

TwinsUK

AF:

0.0812

AC:

301

ALSPAC

AF:

0.0747

AC:

288

ESP6500AA

AF:

0.0137

AC:

ESP6500EA

AF:

0.0769

AC:

636

ExAC

AF:

0.0663

AC:

8013

Asia WGS

AF:

0.0350

AC:

120

AN:

3478

EpiCase

AF:

0.0780

EpiControl

AF:

0.0799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.82

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.13

Eigen

Benign

0.13

Eigen_PC

Benign

0.041

FATHMM_MKL

Uncertain

0.85

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0023

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.5

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-2.7

REVEL

Benign

0.13

Sift

Benign

0.032

Sift4G

Benign

0.51

Polyphen

1.0

Vest4

0.099

MutPred

0.51

Gain of ubiquitination at K196 (P = 0.0797);

MPC

0.22

ClinPred

0.046

GERP RS

2.4

Varity_R

0.65

gMVP

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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