Genetic Variant GALNT14:p.Gln469Lys (chr2-30912318-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024572.4(GALNT14):c.1405C>A(p.Gln469Lys) variant causes a missense change. The variant allele was found at a frequency of 0.233 in 1,613,674 control chromosomes in the GnomAD database, including 44,944 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 0.21 ( 3637 hom., cov: 32)

Exomes 𝑓: 0.24 ( 41307 hom. )

Consequence

GALNT14
NM_024572.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.43

Publications

26 publications found

Variant links:

Genes affected

GALNT14 (HGNC:22946): (polypeptide N-acetylgalactosaminyltransferase 14) This gene encodes a Golgi protein which is a member of the polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-Ts) protein family. These enzymes catalyze the transfer of N-acetyl-D-galactosamine (GalNAc) to the hydroxyl groups on serines and threonines in target peptides. The encoded protein has been shown to transfer GalNAc to large proteins like mucins. Alterations in this gene may play a role in cancer progression and response to chemotherapy. [provided by RefSeq, Jun 2016]

GALNT14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016799569).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4 link	c.1405C>A	p.Gln469Lys	missense_variant	Exon 14 of 15	ENST00000349752.10	NP_078848.2	Q96FL9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT14	ENST00000349752.10 link	c.1405C>A	p.Gln469Lys	missense_variant	Exon 14 of 15	1	NM_024572.4	ENSP00000288988.6		Q96FL9-1

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32543

AN:

151980

Hom.:

3636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.207

GnomAD2 exomes

AF:

0.226

AC:

56846

AN:

251290

AF XY:

0.231

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.170

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.279

Gnomad NFE exome

AF:

0.243

Gnomad OTH exome

AF:

0.221

GnomAD4 exome

AF:

0.235

AC:

343839

AN:

1461576

Hom.:

41307

Cov.:

AF XY:

0.236

AC XY:

171949

AN XY:

727094

show subpopulations

African (AFR)

AF:

0.157

AC:

5257

AN:

33478

American (AMR)

AF:

0.174

AC:

7758

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

5915

AN:

26134

East Asian (EAS)

AF:

0.223

AC:

8867

AN:

39696

South Asian (SAS)

AF:

0.236

AC:

20375

AN:

86252

European-Finnish (FIN)

AF:

0.277

AC:

14780

AN:

53372

Middle Eastern (MID)

AF:

0.224

AC:

1292

AN:

5766

European-Non Finnish (NFE)

AF:

0.239

AC:

265982

AN:

1111782

Other (OTH)

AF:

0.225

AC:

13613

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

13102

26203

39305

52406

65508

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8988

17976

26964

35952

44940

<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:

0.214

AC:

32567

AN:

152098

Hom.:

3637

Cov.:

AF XY:

0.214

AC XY:

15875

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.157

AC:

6508

AN:

41506

American (AMR)

AF:

0.180

AC:

2760

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

839

AN:

3470

East Asian (EAS)

AF:

0.222

AC:

1144

AN:

5150

South Asian (SAS)

AF:

0.236

AC:

1139

AN:

4818

European-Finnish (FIN)

AF:

0.288

AC:

3046

AN:

10580

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16418

AN:

67968

Other (OTH)

AF:

0.212

AC:

446

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1323

2646

3969

5292

6615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.233

Hom.:

19354

Bravo

AF:

0.205

TwinsUK

AF:

0.234

AC:

867

ALSPAC

AF:

0.247

AC:

951

ESP6500AA

AF:

0.164

AC:

722

ESP6500EA

AF:

0.242

AC:

2081

ExAC

AF:

0.226

AC:

27435

Asia WGS

AF:

0.239

AC:

834

AN:

3478

EpiCase

AF:

0.246

EpiControl

AF:

0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.015

.;T;.

Eigen

Uncertain

0.44

Eigen_PC

Uncertain

0.47

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.60

T;T;T

MetaRNN

Benign

0.0017

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

.;M;.

PhyloP100

6.4

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-1.2

N;N;N

REVEL

Benign

0.092

Sift

Benign

0.40

T;T;T

Sift4G

Benign

0.66

T;T;T

Polyphen

0.96

D;B;.

Vest4

0.18

MPC

0.87

ClinPred

0.034

GERP RS

5.0

Varity_R

0.66

gMVP

0.67

Mutation Taster

=87/13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over