rs4846913

Variant names:

• chr1-230158968-C-A
• rs4846913
• NM_004481.5:c.127-19250C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-230158968-C-A
• chr1-230158968-C-T

Variant summary

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

The NM_004481.5(GALNT2):​c.127-19250C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,082 control chromosomes in the GnomAD database, including 18,203 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 0.45 (18203 hom., cov: 33)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 33 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004481.5. 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_004481.5	MANE Select	c.127-19250C>A		intron	N/A	NP_004472.1
	GALNT2	NM_001291866.2		c.13-19250C>A		intron	N/A	NP_001278795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT2	ENST00000366672.5	TSL:1 MANE Select	c.127-19250C>A		intron	N/A	ENSP00000355632.4
	GALNT2	ENST00000494106.1	TSL:5	n.90-19250C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67774 AN: 151964 Hom.: 18199 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.446 AC: 67786 AN: 152082 Hom.: 18203 Cov.: 33 AF XY: 0.443 AC XY: 32894 AN XY: 74334

African (AFR) AF: 0.137 AC: 5693 AN: 41488

American (AMR) AF: 0.546 AC: 8352 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2120 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1041 AN: 5160

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5693 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.604 AC: 41074 AN: 67972

Other (OTH) AF: 0.504 AC: 1063 AN: 2110

Alfa AF: 0.520 Hom.: 28822

Bravo AF: 0.433

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.71
DANN	Benign	0.53
PhyloP100		-0.34
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: rs4846913; hg19: chr1-230294715;