Genetic Variant GALNT14:c.129+144A>T (chr2-31137814-T-A) – 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.129+144A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,026,200 control chromosomes in the GnomAD database, including 37,596 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 0.28 ( 6098 hom., cov: 33)

Exomes 𝑓: 0.26 ( 31498 hom. )

Consequence

GALNT14
NM_024572.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

5 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 (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4 link	c.129+144A>T		intron_variant	Intron 1 of 14	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.129+144A>T		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6		Q96FL9-1

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42807

AN:

151912

Hom.:

6082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.265

AC:

231241

AN:

874172

Hom.:

31498

AF XY:

0.265

AC XY:

116627

AN XY:

439696

show subpopulations

African (AFR)

AF:

0.336

AC:

6739

AN:

20040

American (AMR)

AF:

0.261

AC:

5379

AN:

20572

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

4127

AN:

16266

East Asian (EAS)

AF:

0.295

AC:

9679

AN:

32828

South Asian (SAS)

AF:

0.299

AC:

16365

AN:

54806

European-Finnish (FIN)

AF:

0.253

AC:

10470

AN:

41404

Middle Eastern (MID)

AF:

0.328

AC:

1115

AN:

3402

European-Non Finnish (NFE)

AF:

0.258

AC:

166460

AN:

645202

Other (OTH)

AF:

0.275

AC:

10907

AN:

39652

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

8377

16753

25130

33506

41883

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4790

9580

14370

19160

23950

<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:

0.282

AC:

42853

AN:

152028

Hom.:

6098

Cov.:

AF XY:

0.282

AC XY:

20950

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.334

AC:

13835

AN:

41464

American (AMR)

AF:

0.264

AC:

4043

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.261

AC:

905

AN:

3472

East Asian (EAS)

AF:

0.276

AC:

1416

AN:

5126

South Asian (SAS)

AF:

0.297

AC:

1433

AN:

4818

European-Finnish (FIN)

AF:

0.255

AC:

2697

AN:

10584

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.260

AC:

17636

AN:

67954

Other (OTH)

AF:

0.277

AC:

584

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1614

3228

4843

6457

8071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.266

Hom.:

680

Bravo

AF:

0.284

Asia WGS

AF:

0.277

AC:

961

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

5.2

(source)

DANN

Benign

0.87

PhyloP100

-0.031

PromoterAI

-0.059

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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