rs3213495

Variant names:

• chr1-230280292-G-A
• rs3213495
• NM_004481.5:c.*834G>A

Variant summary

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

The NM_004481.5(GALNT2):​c.*834G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 297,766 control chromosomes in the GnomAD database, including 4,314 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 0.16 (2350 hom., cov: 33)
  • Exomes 𝑓: 0.14 (1964 hom.)
• Consequence: GALNT2 NM_004481.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 10 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

ENSG00000224407 (HGNC:40252):

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 (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.*834G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.*834G>A		3_prime_UTR_variant	Exon 16 of 16		NP_001278795.1
GALNT2	XM_017000964.3	c.*834G>A		3_prime_UTR_variant	Exon 17 of 17		XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.*834G>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_004481.5	ENSP00000355632.4
GALNT2	ENST00000485438.1	n.2202G>A		non_coding_transcript_exon_variant	Exon 6 of 6	5
ENSG00000224407	ENST00000414640.1	n.*20C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24475 AN: 152082 Hom.: 2340 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.157

GnomAD4 exome AF: 0.138 AC: 20024 AN: 145566 Hom.: 1964 Cov.: 0 AF XY: 0.136 AC XY: 10602 AN XY: 77858

African (AFR) AF: 0.203 AC: 972 AN: 4798

American (AMR) AF: 0.181 AC: 1752 AN: 9668

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 244 AN: 3256

East Asian (EAS) AF: 0.449 AC: 3435 AN: 7644

South Asian (SAS) AF: 0.107 AC: 2722 AN: 25362

European-Finnish (FIN) AF: 0.119 AC: 643 AN: 5422

Middle Eastern (MID) AF: 0.0792 AC: 41 AN: 518

European-Non Finnish (NFE) AF: 0.113 AC: 9258 AN: 81620

Other (OTH) AF: 0.131 AC: 957 AN: 7278

GnomAD4 genome AF: 0.161 AC: 24521 AN: 152200 Hom.: 2350 Cov.: 33 AF XY: 0.162 AC XY: 12088 AN XY: 74406

African (AFR) AF: 0.213 AC: 8839 AN: 41538

American (AMR) AF: 0.184 AC: 2822 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2221 AN: 5158

South Asian (SAS) AF: 0.124 AC: 598 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1394 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8006 AN: 67998

Other (OTH) AF: 0.155 AC: 329 AN: 2116

Alfa AF: 0.129 Hom.: 2383

Bravo AF: 0.171

Asia WGS AF: 0.245 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.010
DANN	Benign	0.87
PhyloP100		-2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3213495; hg19: chr1-230416038;