Variant chr7-100159989-G-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_024637.5(GAL3ST4):c.1400C>T(p.Ala467Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,612,990 control chromosomes in the GnomAD database, including 243,292 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 0.50 ( 19675 hom., cov: 30)

Exomes 𝑓: 0.55 ( 223617 hom. )

Consequence

GAL3ST4
NM_024637.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.527

Variant links:

Genes affected

GAL3ST4 (HGNC:24145): (galactose-3-O-sulfotransferase 4) This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate to the C-3' position of galactose residues in O-linked glycoproteins. This enzyme is highly specific for core 1 structures, with asialofetuin, Gal-beta-1,3-GalNAc and Gal-beta-1,3 (GlcNAc-beta-1,6)GalNAc being good substrates. [provided by RefSeq, Jul 2008]

GAL3ST4 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=6.1614282E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAL3ST4	NM_024637.5 linkuse as main transcript	c.1400C>T	p.Ala467Val	missense_variant	4/4	ENST00000360039.9	NP_078913.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAL3ST4	ENST00000360039.9 linkuse as main transcript	c.1400C>T	p.Ala467Val	missense_variant	4/4	1	NM_024637.5	ENSP00000353142	P1	Q96RP7-1

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

75970

AN:

151700

Hom.:

19661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.640

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.512

GnomAD3 exomes

AF:

0.540

AC:

135577

AN:

250978

Hom.:

37252

AF XY:

0.550

AC XY:

74628

AN XY:

135678

show subpopulations

Gnomad AFR exome

AF:

0.371

Gnomad AMR exome

AF:

0.445

Gnomad ASJ exome

AF:

0.611

Gnomad EAS exome

AF:

0.644

Gnomad SAS exome

AF:

0.594

Gnomad FIN exome

AF:

0.565

Gnomad NFE exome

AF:

0.551

Gnomad OTH exome

AF:

0.552

GnomAD4 exome

AF:

0.551

AC:

805340

AN:

1461172

Hom.:

223617

Cov.:

AF XY:

0.555

AC XY:

403087

AN XY:

726918

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.448

Gnomad4 ASJ exome

AF:

0.609

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.561

Gnomad4 NFE exome

AF:

0.553

Gnomad4 OTH exome

AF:

0.550

GnomAD4 genome

AF:

0.501

AC:

76025

AN:

151818

Hom.:

19675

Cov.:

AF XY:

0.505

AC XY:

37423

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.372

Gnomad4 AMR

AF:

0.452

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.641

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.553

Gnomad4 OTH

AF:

0.512

Alfa

AF:

0.548

Hom.:

57718

Bravo

AF:

0.488

TwinsUK

AF:

0.564

AC:

2093

ALSPAC

AF:

0.549

AC:

2116

ESP6500AA

AF:

0.386

AC:

1699

ESP6500EA

AF:

0.568

AC:

4887

ExAC

AF:

0.537

AC:

65198

Asia WGS

AF:

0.606

AC:

2105

AN:

3478

EpiCase

AF:

0.556

EpiControl

AF:

0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0038

T;T

Eigen

Benign

-0.23

Eigen_PC

Benign

-0.055

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.60

.;T

MetaRNN

Benign

0.0000062

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.6

L;L

MutationTaster

Benign

0.071

P;P;P;P;P

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.97

N;N

REVEL

Benign

0.024

Sift

Benign

0.041

D;D

Sift4G

Benign

0.11

T;T

Polyphen

0.0080

B;B

Vest4

0.027

MPC

0.11

ClinPred

0.0096

GERP RS

5.0

Varity_R

0.082

gMVP

0.46

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