chr1-230221071-A-G

Variant names:

• chr1-230221071-A-G
• rs10864732
• NM_004481.5:c.375-14943A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004481.5(GALNT2):​c.375-14943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,100 control chromosomes in the GnomAD database, including 27,304 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 0.57 (27304 hom., cov: 32)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 3 publications found

Genes affected

GALNT2 (HGNC:4124): (polypeptide N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

GALNT2 Gene-Disease associations (from GenCC):

• congenital disorder of glycosylation, type iit

  Inheritance: AR Classification: STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.375-14943A>G		intron_variant	Intron 3 of 15	ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.261-14943A>G		intron_variant	Intron 3 of 15		NP_001278795.1
GALNT2	XM_017000964.3	c.282-14943A>G		intron_variant	Intron 4 of 16		XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.375-14943A>G		intron_variant	Intron 3 of 15	1	NM_004481.5	ENSP00000355632.4
GALNT2	ENST00000494106.1	n.338-14943A>G		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86421 AN: 151982 Hom.: 27262 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.569 AC: 86524 AN: 152100 Hom.: 27304 Cov.: 32 AF XY: 0.569 AC XY: 42337 AN XY: 74352

African (AFR) AF: 0.820 AC: 34033 AN: 41510

American (AMR) AF: 0.631 AC: 9638 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1544 AN: 3464

East Asian (EAS) AF: 0.898 AC: 4643 AN: 5172

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4812

European-Finnish (FIN) AF: 0.397 AC: 4199 AN: 10580

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28440 AN: 67968

Other (OTH) AF: 0.541 AC: 1141 AN: 2108

Alfa AF: 0.465 Hom.: 26903

Bravo AF: 0.600

Asia WGS AF: 0.687 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		-0.010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10864732; hg19: chr1-230356817;