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

Variant summary

Our verdict is Benign. Variant got -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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.226

AC:

56846

AN:

251290

Hom.:

6647

AF XY:

0.231

AC XY:

31415

AN XY:

135804

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 SAS exome

AF:

0.233

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

Gnomad4 AFR exome

AF:

0.157

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.223

Gnomad4 SAS exome

AF:

0.236

Gnomad4 FIN exome

AF:

0.277

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.214

AC:

32567

AN:

152098

Hom.:

3637

Cov.:

AF XY:

0.214

AC XY:

15875

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.236

Hom.:

10634

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

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;.

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

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