rs1043908

chr1-230281548-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004481.5(GALNT2):c.*2090A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,070 control chromosomes in the GnomAD database, including 1,509 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 0.13 (1509 hom., cov: 31)
  • Exomes 𝑓: 0.084 (0 hom.)
• Consequence: GALNT2 NM_004481.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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 (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT2	NM_004481.5	c.*2090A>G		3_prime_UTR_variant	16/16	ENST00000366672.5
GALNT2	NM_001291866.2	c.*2090A>G		3_prime_UTR_variant	16/16
GALNT2	XM_017000964.3	c.*2090A>G		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT2	ENST00000366672.5	c.*2090A>G		3_prime_UTR_variant	16/16	1	NM_004481.5	P1
	ENST00000414640.1	n.346T>C		non_coding_transcript_exon_variant	1/2	3
GALNT2	ENST00000485438.1	n.3458A>G		non_coding_transcript_exon_variant	6/6	5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20137 AN: 151654 Hom.: 1508 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.138

GnomAD4 exome AF: 0.0839 AC: 25 AN: 298 Hom.: 0 Cov.: 0 AF XY: 0.0737 AC XY: 14 AN XY: 190

Gnomad4 AFR exome AF: 0.125

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0946

Gnomad4 NFE exome AF: 0.0345

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.133 AC: 20168 AN: 151772 Hom.: 1509 Cov.: 31 AF XY: 0.132 AC XY: 9808 AN XY: 74182

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0940

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.138

Alfa AF: 0.111 Hom.: 1464

Bravo AF: 0.135

Asia WGS AF: 0.123 AC: 429 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	0.31
Dann	Benign	0.74

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: rs1043908; hg19: chr1-230417294;