9-98808054-A-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024642.5(GALNT12):c.356A>T(p.Glu119Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 1,579,888 control chromosomes in the GnomAD database, including 6,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E119K) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.063 ( 386 hom., cov: 32)

Exomes 𝑓: 0.085 ( 5941 hom. )

Consequence

GALNT12
NM_024642.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 8.07

Publications

14 publications found

Variant links:

Genes affected

GALNT12 (HGNC:19877): (polypeptide N-acetylgalactosaminyltransferase 12) This gene encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial step of O-linked protein glycosylation. Mutations in this gene are associated with an increased susceptibility to colorectal cancer.[provided by RefSeq, Mar 2011]

GALNT12 Gene-Disease associations (from GenCC):

colorectal cancer, susceptibility to, 1
Inheritance: AD Classification: LIMITED Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

GALNT12 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018546879).

BP6

Variant 9-98808054-A-T is Benign according to our data. Variant chr9-98808054-A-T is described in ClinVar as Benign. ClinVar VariationId is 485633.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024642.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	NM_024642.5	MANE Select	c.356A>T	p.Glu119Val	missense	Exon 1 of 10	NP_078918.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	ENST00000375011.4	TSL:1 MANE Select	c.356A>T	p.Glu119Val	missense	Exon 1 of 10	ENSP00000364150.3
	GALNT12	ENST00000610463.1	TSL:4	n.50A>T		non_coding_transcript_exon	Exon 1 of 4	ENSP00000477657.1

Frequencies

GnomAD3 genomes

AF:

0.0635

AC:

9648

AN:

151972

Hom.:

386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0161

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0469

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.000581

Gnomad SAS

AF:

0.0249

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0975

Gnomad OTH

AF:

0.0590

GnomAD2 exomes

AF:

0.0582

AC:

11071

AN:

190346

AF XY:

0.0591

show subpopulations

Gnomad AFR exome

AF:

0.0120

Gnomad AMR exome

AF:

0.0285

Gnomad ASJ exome

AF:

0.0349

Gnomad EAS exome

AF:

0.000262

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.0879

Gnomad OTH exome

AF:

0.0676

GnomAD4 exome

AF:

0.0855

AC:

122023

AN:

1427798

Hom.:

5941

Cov.:

AF XY:

0.0839

AC XY:

59361

AN XY:

707484

show subpopulations

African (AFR)

AF:

0.0118

AC:

389

AN:

33094

American (AMR)

AF:

0.0302

AC:

1231

AN:

40764

Ashkenazi Jewish (ASJ)

AF:

0.0354

AC:

901

AN:

25456

East Asian (EAS)

AF:

0.000181

AC:

AN:

38652

South Asian (SAS)

AF:

0.0311

AC:

2540

AN:

81704

European-Finnish (FIN)

AF:

0.115

AC:

5319

AN:

46290

Middle Eastern (MID)

AF:

0.0444

AC:

206

AN:

4642

European-Non Finnish (NFE)

AF:

0.0978

AC:

107365

AN:

1098008

Other (OTH)

AF:

0.0687

AC:

4065

AN:

59188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

4974

9949

14923

19898

24872

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3862

7724

11586

15448

19310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0634

AC:

9649

AN:

152090

Hom.:

386

Cov.:

AF XY:

0.0621

AC XY:

4618

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0161

AC:

667

AN:

41534

American (AMR)

AF:

0.0468

AC:

715

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0337

AC:

117

AN:

3468

East Asian (EAS)

AF:

0.000582

AC:

AN:

5154

South Asian (SAS)

AF:

0.0253

AC:

122

AN:

4822

European-Finnish (FIN)

AF:

0.116

AC:

1229

AN:

10554

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0975

AC:

6624

AN:

67954

Other (OTH)

AF:

0.0584

AC:

123

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

459

918

1376

1835

2294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0822

Hom.:

175

Bravo

AF:

0.0546

TwinsUK

AF:

0.0957

AC:

355

ALSPAC

AF:

0.0991

AC:

382

ESP6500AA

AF:

0.0159

AC:

ESP6500EA

AF:

0.0793

AC:

664

ExAC

AF:

0.0471

AC:

5540

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Jun 22, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Hereditary cancer-predisposing syndrome

Benign:2

Jan 10, 2025

Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The missense variant NM_024642.5(GALNT12):c.356A>T (p.Glu119Val) has been reported to ClinVar as Benign with a status of (2 stars) criteria provided, multiple submitters, no conflicts (Variation ID 485633 as of 2025-01-02). The p.Glu119Val variant is observed in 143/5,008 (2.8554%) alleles from individuals of 1kG All background in 1kG, indicating it is a common benign variant. There is a moderate physicochemical difference between glutamic acid and valine. The glutamic acid residue at codon 119 of GALNT12 is conserved in all mammalian species. For these reasons, this variant has been classified as Benign

Jul 10, 2025

GeneKor MSA

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

Aug 12, 2016

Ambry Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Colorectal cancer, susceptibility to, 1

Benign:1

Sep 15, 2021

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

GALNT12-related disorder

Benign:1

Apr 28, 2021

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

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 v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.21

CADD

Pathogenic

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.35

Eigen

Uncertain

0.35

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.9

PhyloP100

8.1

PrimateAI

Uncertain

0.73

PROVEAN

Uncertain

-3.9

REVEL

Uncertain

0.36

Sift

Pathogenic

0.0

Sift4G

Uncertain

0.0020

Polyphen

0.79

Vest4

0.26

MPC

0.45

ClinPred

0.068

GERP RS

3.7

PromoterAI

-0.025

Neutral

(source)

Varity_R

0.89

gMVP

0.72

Mutation Taster

=77/23

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over