Genetic Variant GALNT5:c.1621+132G>T (chr2-157284580-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_014568.3(GALNT5):c.1621+132G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 690,814 control chromosomes in the GnomAD database, including 5,862 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 0.14 ( 4188 hom., cov: 33)

Exomes 𝑓: 0.033 ( 1674 hom. )

Consequence

GALNT5
NM_014568.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260

Publications

1 publications found

Variant links:

Genes affected

GALNT5 (HGNC:4127): (polypeptide N-acetylgalactosaminyltransferase 5) The protein encoded by this gene is a membrane-bound polypeptide N-acetylgalactosaminyltransferase that is found in the Golgi. The encoded protein catalyzes the first step in the mucin-type O-glycosylation of Golgi proteins, transfering an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. [provided by RefSeq, Aug 2016]

GALNT5 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT5	NM_014568.3 link	c.1621+132G>T		intron_variant	Intron 2 of 9	ENST00000259056.5	NP_055383.1	Q7Z7M9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT5	ENST00000259056.5 link	c.1621+132G>T		intron_variant	Intron 2 of 9	1	NM_014568.3	ENSP00000259056.4		Q7Z7M9

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

20928

AN:

152066

Hom.:

4163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.0646

Gnomad ASJ

AF:

0.0377

Gnomad EAS

AF:

0.000961

Gnomad SAS

AF:

0.0265

Gnomad FIN

AF:

0.00471

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.0333

AC:

17946

AN:

538630

Hom.:

1674

AF XY:

0.0312

AC XY:

8859

AN XY:

283948

show subpopulations

African (AFR)

AF:

0.436

AC:

6475

AN:

14854

American (AMR)

AF:

0.0382

AC:

1084

AN:

28380

Ashkenazi Jewish (ASJ)

AF:

0.0356

AC:

566

AN:

15904

East Asian (EAS)

AF:

0.000381

AC:

AN:

31484

South Asian (SAS)

AF:

0.0260

AC:

1344

AN:

51712

European-Finnish (FIN)

AF:

0.00838

AC:

272

AN:

32460

Middle Eastern (MID)

AF:

0.0573

AC:

215

AN:

3750

European-Non Finnish (NFE)

AF:

0.0193

AC:

6374

AN:

330778

Other (OTH)

AF:

0.0547

AC:

1604

AN:

29308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

674

1349

2023

2698

3372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

148

296

444

592

740

<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:

0.138

AC:

20997

AN:

152184

Hom.:

4188

Cov.:

AF XY:

0.133

AC XY:

9880

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.438

AC:

18154

AN:

41448

American (AMR)

AF:

0.0645

AC:

987

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0377

AC:

131

AN:

3472

East Asian (EAS)

AF:

0.000963

AC:

AN:

5192

South Asian (SAS)

AF:

0.0267

AC:

129

AN:

4826

European-Finnish (FIN)

AF:

0.00471

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0183

AC:

1247

AN:

68022

Other (OTH)

AF:

0.111

AC:

234

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

654

1309

1963

2618

3272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.0274

Hom.:

Bravo

AF:

0.158

Asia WGS

AF:

0.0440

AC:

153

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.2

(source)

DANN

Benign

0.64

PhyloP100

0.026

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