Variant chr2-64458296-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000238875.10(LGALSL):c.387T>C(p.Leu129Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00823 in 1,613,840 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0070 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0084 ( 76 hom. )

Consequence

LGALSL
ENST00000238875.10 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0910

Variant links:

Genes affected

LGALSL (HGNC:25012): (galectin like) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]

LGALSL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036326945).

BP6

Variant 2-64458296-T-C is Benign according to our data. Variant chr2-64458296-T-C is described in ClinVar as [Benign]. Clinvar id is 782084.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.091 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALSL	NM_014181.3 linkuse as main transcript	c.387T>C	p.Leu129Leu	synonymous_variant	5/5	ENST00000238875.10	NP_054900.2	Q3ZCW2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALSL	ENST00000238875.10 linkuse as main transcript	c.387T>C	p.Leu129Leu	synonymous_variant	5/5	1	NM_014181.3	ENSP00000238875.4		Q3ZCW2

Frequencies

GnomAD3 genomes

AF:

0.00701

AC:

1068

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00628

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00911

Gnomad FIN

AF:

0.00611

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0112

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.00765

AC:

1920

AN:

250874

Hom.:

AF XY:

0.00816

AC XY:

1107

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00572

Gnomad ASJ exome

AF:

0.0101

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00830

Gnomad FIN exome

AF:

0.00698

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.00799

GnomAD4 exome

AF:

0.00836

AC:

12214

AN:

1461474

Hom.:

Cov.:

AF XY:

0.00853

AC XY:

6205

AN XY:

727016

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.00674

Gnomad4 ASJ exome

AF:

0.0113

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.00868

Gnomad4 FIN exome

AF:

0.00739

Gnomad4 NFE exome

AF:

0.00890

Gnomad4 OTH exome

AF:

0.00808

GnomAD4 genome

AF:

0.00701

AC:

1068

AN:

152366

Hom.:

Cov.:

AF XY:

0.00707

AC XY:

527

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00627

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00911

Gnomad4 FIN

AF:

0.00611

Gnomad4 NFE

AF:

0.0112

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.0103

Hom.:

Bravo

AF:

0.00591

TwinsUK

AF:

0.00755

AC:

ALSPAC

AF:

0.00882

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.0102

AC:

ExAC

AF:

0.00828

AC:

1005

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.0101

EpiControl

AF:

0.00972

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.056

BayesDel_noAF

Pathogenic

0.16

CADD

Benign

1.1

DANN

Benign

0.67

DEOGEN2

Benign

0.0076

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.59

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0036

MetaSVM

Uncertain

-0.27

MutationTaster

Benign

1.0

D;N

PROVEAN

Benign

3.4

REVEL

Uncertain

0.30

Sift

Benign

1.0

Sift4G

Benign

1.0

Vest4

0.20

MVP

0.26

ClinPred

0.0049

GERP RS

-5.4

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over