Genetic Variant GALNT14:c.300-68C>T (chr2-30966370-G-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.300-68C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,180,702 control chromosomes in the GnomAD database, including 15,915 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 0.16 ( 1953 hom., cov: 32)

Exomes 𝑓: 0.16 ( 13962 hom. )

Consequence

GALNT14
NM_024572.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4 link	c.300-68C>T		intron_variant	Intron 2 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.300-68C>T		intron_variant	Intron 2 of 14	1	NM_024572.4	ENSP00000288988.6		Q96FL9-1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23644

AN:

151966

Hom.:

1953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0686

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.159

AC:

163727

AN:

1028618

Hom.:

13962

AF XY:

0.159

AC XY:

83679

AN XY:

526508

show subpopulations

African (AFR)

AF:

0.166

AC:

4189

AN:

25292

American (AMR)

AF:

0.134

AC:

5321

AN:

39654

Ashkenazi Jewish (ASJ)

AF:

0.0717

AC:

1615

AN:

22518

East Asian (EAS)

AF:

0.348

AC:

12803

AN:

36760

South Asian (SAS)

AF:

0.159

AC:

11734

AN:

73734

European-Finnish (FIN)

AF:

0.152

AC:

7795

AN:

51148

Middle Eastern (MID)

AF:

0.0921

AC:

450

AN:

4886

European-Non Finnish (NFE)

AF:

0.155

AC:

113188

AN:

728826

Other (OTH)

AF:

0.145

AC:

6632

AN:

45800

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

6577

13154

19732

26309

32886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3516

7032

10548

14064

17580

<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:

0.156

AC:

23657

AN:

152084

Hom.:

1953

Cov.:

AF XY:

0.154

AC XY:

11478

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.165

AC:

6864

AN:

41480

American (AMR)

AF:

0.129

AC:

1973

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0686

AC:

238

AN:

3470

East Asian (EAS)

AF:

0.318

AC:

1635

AN:

5148

South Asian (SAS)

AF:

0.158

AC:

764

AN:

4828

European-Finnish (FIN)

AF:

0.143

AC:

1510

AN:

10586

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10238

AN:

67972

Other (OTH)

AF:

0.135

AC:

285

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1017

2034

3050

4067

5084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.153

Hom.:

726

Bravo

AF:

0.156

Asia WGS

AF:

0.236

AC:

821

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.023

(source)

DANN

Benign

0.28

PhyloP100

-2.0

Mutation Taster

=100/0

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