dbSNP rs4761874: GALNT6:c.1167+426G>A (chr12-51360295-C-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_007210.4(GALNT6):c.1167+426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 153,354 control chromosomes in the GnomAD database, including 5,539 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 0.27 ( 5501 hom., cov: 31)

Exomes 𝑓: 0.23 ( 38 hom. )

Consequence

GALNT6
NM_007210.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.658

Publications

7 publications found

Variant links:

Genes affected

GALNT6 (HGNC:4128): (polypeptide N-acetylgalactosaminyltransferase 6) This gene encodes a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. GalNAc-Ts initiate mucin-type O-linked glycosylation in the Golgi apparatus by catalyzing the transfer of GalNAc to serine and threonine residues on target proteins. They are characterized by an N-terminal transmembrane domain, a stem region, a lumenal catalytic domain containing a GT1 motif and Gal/GalNAc transferase motif, and a C-terminal ricin/lectin-like domain. GalNAc-Ts have different, but overlapping, substrate specificities and patterns of expression. The encoded protein is capable of glycosylating fibronectin peptide in vitro and is expressed in a fibroblast cell line, indicating that it may be involved in the synthesis of oncofetal fibronectin. [provided by RefSeq, Jul 2008]

GALNT6 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT6	NM_007210.4 link	c.1167+426G>A		intron_variant	Intron 7 of 11	ENST00000356317.8	NP_009141.2	Q8NCL4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GALNT6	ENST00000356317.8 link	c.1167+426G>A	intron_variant	Intron 7 of 11	1	NM_007210.4	ENSP00000348668.2	Q8NCL4
GALNT6	ENST00000543196.6 link	c.1167+426G>A	intron_variant	Intron 6 of 10	1		ENSP00000444171.1	Q8NCL4
GALNT6	ENST00000603641.1 link	n.1050-963G>A	intron_variant	Intron 4 of 8	1		ENSP00000474670.1	S4R3S5
GALNT6	ENST00000603680.5 link	n.-69G>A	upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40272

AN:

151780

Hom.:

5499

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.230

AC:

335

AN:

1456

Hom.:

AF XY:

0.231

AC XY:

172

AN XY:

744

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.0984

AC:

AN:

122

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

AN:

East Asian (EAS)

AF:

0.0714

AC:

AN:

South Asian (SAS)

AF:

0.217

AC:

AN:

European-Finnish (FIN)

AF:

0.292

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.251

AC:

279

AN:

1110

Other (OTH)

AF:

0.206

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.265

AC:

40306

AN:

151898

Hom.:

5501

Cov.:

AF XY:

0.262

AC XY:

19453

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.303

AC:

12544

AN:

41398

American (AMR)

AF:

0.207

AC:

3163

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

853

AN:

3472

East Asian (EAS)

AF:

0.116

AC:

597

AN:

5166

South Asian (SAS)

AF:

0.228

AC:

1096

AN:

4814

European-Finnish (FIN)

AF:

0.318

AC:

3347

AN:

10518

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.263

AC:

17871

AN:

67938

Other (OTH)

AF:

0.254

AC:

535

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1484

2968

4452

5936

7420

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<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.:

5948

Bravo

AF:

0.259

Asia WGS

AF:

0.178

AC:

618

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.52

PhyloP100

0.66

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