rs3213495

chr1-230280292-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GALNT2	NM_004481.5	c.*834G>A		3_prime_UTR_variant	16/16	ENST00000366672.5
GALNT2	NM_001291866.2	c.*834G>A		3_prime_UTR_variant	16/16
GALNT2	XM_017000964.3	c.*834G>A		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT2	ENST00000366672.5	c.*834G>A		3_prime_UTR_variant	16/16	1	NM_004481.5	P1
GALNT2	ENST00000485438.1	n.2202G>A		non_coding_transcript_exon_variant	6/6	5
	ENST00000414640.1			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

Gnomad4 AFR exome AF: 0.203

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.0749

Gnomad4 EAS exome AF: 0.449

Gnomad4 SAS exome AF: 0.107

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.113

Gnomad4 OTH exome AF: 0.131

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.155

Alfa AF: 0.125 Hom.: 1770

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs3213495; hg19: chr1-230416038;