1-230063651-C-T

Variant names:

• chr1-230063651-C-T
• rs12040273
• NM_001291866.2:c.12+5573C>T

Variant summary

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

The NM_001291866.2(GALNT2):​c.12+5573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,160 control chromosomes in the GnomAD database, including 10,532 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 (10532 hom., cov: 33)
• Consequence: GALNT2 NM_001291866.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291866.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT2	NM_001291866.2		c.12+5573C>T		intron	N/A	NP_001278795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT2	ENST00000494106.1	TSL:5	n.89+5573C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41506 AN: 152042 Hom.: 10500 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.273 AC: 41596 AN: 152160 Hom.: 10532 Cov.: 33 AF XY: 0.271 AC XY: 20142 AN XY: 74402

African (AFR) AF: 0.671 AC: 27830 AN: 41470

American (AMR) AF: 0.171 AC: 2614 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1834 AN: 5180

South Asian (SAS) AF: 0.245 AC: 1184 AN: 4828

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10594

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6387 AN: 68012

Other (OTH) AF: 0.226 AC: 476 AN: 2108

Alfa AF: 0.160 Hom.: 6937

Bravo AF: 0.299

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.22
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12040273; hg19: chr1-230199398;