Variant chr1-236537507-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_201544.4(LGALS8):c.56T>A(p.Phe19Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,564,154 control chromosomes in the GnomAD database, including 347,465 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.61 ( 29286 hom., cov: 32)

Exomes 𝑓: 0.66 ( 318179 hom. )

Consequence

LGALS8
NM_201544.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.11

Variant links:

Genes affected

LGALS8 (HGNC:6569): (galectin 8) This gene encodes a member of the galectin family. Galectins are beta-galactoside-binding animal lectins with conserved carbohydrate recognition domains. The galectins have been implicated in many essential functions including development, differentiation, cell-cell adhesion, cell-matrix interaction, growth regulation, apoptosis, and RNA splicing. This gene is widely expressed in tumoral tissues and seems to be involved in integrin-like cell interactions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

LGALS8 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=4.5207125E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGALS8	NM_201544.4 linkuse as main transcript	c.56T>A	p.Phe19Tyr	missense_variant	3/10	ENST00000366584.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS8	ENST00000366584.9 linkuse as main transcript	c.56T>A	p.Phe19Tyr	missense_variant	3/10	1	NM_201544.4	P1	O00214-1

Frequencies

GnomAD3 genomes

AF:

0.611

AC:

92806

AN:

151824

Hom.:

29267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.574

Gnomad ASJ

AF:

0.609

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.607

GnomAD3 exomes

AF:

0.611

AC:

152862

AN:

250140

Hom.:

48131

AF XY:

0.610

AC XY:

82517

AN XY:

135244

show subpopulations

Gnomad AFR exome

AF:

0.489

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.600

Gnomad EAS exome

AF:

0.486

Gnomad SAS exome

AF:

0.472

Gnomad FIN exome

AF:

0.736

Gnomad NFE exome

AF:

0.686

Gnomad OTH exome

AF:

0.629

GnomAD4 exome

AF:

0.664

AC:

937110

AN:

1412210

Hom.:

318179

Cov.:

AF XY:

0.658

AC XY:

464228

AN XY:

705084

show subpopulations

Gnomad4 AFR exome

AF:

0.484

Gnomad4 AMR exome

AF:

0.533

Gnomad4 ASJ exome

AF:

0.599

Gnomad4 EAS exome

AF:

0.472

Gnomad4 SAS exome

AF:

0.478

Gnomad4 FIN exome

AF:

0.739

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.637

GnomAD4 genome

AF:

0.611

AC:

92872

AN:

151944

Hom.:

29286

Cov.:

AF XY:

0.608

AC XY:

45190

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.574

Gnomad4 ASJ

AF:

0.609

Gnomad4 EAS

AF:

0.485

Gnomad4 SAS

AF:

0.459

Gnomad4 FIN

AF:

0.751

Gnomad4 NFE

AF:

0.690

Gnomad4 OTH

AF:

0.605

Alfa

AF:

0.665

Hom.:

25638

Bravo

AF:

0.591

TwinsUK

AF:

0.701

AC:

2598

ALSPAC

AF:

0.693

AC:

2672

ESP6500AA

AF:

0.493

AC:

2173

ESP6500EA

AF:

0.683

AC:

5870

ExAC

AF:

0.609

AC:

73977

Asia WGS

AF:

0.452

AC:

1576

AN:

3478

EpiCase

AF:

0.673

EpiControl

AF:

0.664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.77

DEOGEN2

Benign

0.011

.;.;.;T;.;T;.;.;T;T;.;T;.;T;T;T

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.50

FATHMM_MKL

Benign

0.25

LIST_S2

Benign

0.22

T;T;.;T;.;T;.;T;.;T;T;.;T;T;T;.

MetaRNN

Benign

0.0000045

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.72

.;.;N;.;N;.;N;.;N;.;N;N;.;.;N;.

MutationTaster

Benign

1.0

P;P;P;P;P;P;P;P;P;P

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.29

N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.12

Sift

Benign

1.0

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

Sift4G

Benign

0.89

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.0, 0.0010

.;.;B;.;B;.;B;.;B;B;B;B;.;.;B;B

Vest4

0.098, 0.13, 0.10, 0.14, 0.17, 0.10, 0.14, 0.13, 0.14, 0.12

MPC

0.060

ClinPred

0.0080

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.21

gMVP

0.84

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