1-230281548-A-G

Variant names:

• chr1-230281548-A-G
• rs1043908
• NM_004481.5:c.*2090A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.198 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.*2090A>G		3_prime_UTR	Exon 16 of 16	NP_004472.1
	GALNT2	NM_001291866.2		c.*2090A>G		3_prime_UTR	Exon 16 of 16	NP_001278795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT2	ENST00000366672.5	TSL:1 MANE Select	c.*2090A>G		3_prime_UTR	Exon 16 of 16	ENSP00000355632.4
	GALNT2	ENST00000868579.1		c.*2090A>G		3_prime_UTR	Exon 16 of 16	ENSP00000538638.1
	GALNT2	ENST00000868580.1		c.*2090A>G		3_prime_UTR	Exon 14 of 14	ENSP00000538639.1

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

African (AFR) AF: 0.125 AC: 1 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0946 AC: 21 AN: 222

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0345 AC: 2 AN: 58

Other (OTH) AF: 0.125 AC: 1 AN: 8

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

African (AFR) AF: 0.202 AC: 8358 AN: 41366

American (AMR) AF: 0.0940 AC: 1435 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3462

East Asian (EAS) AF: 0.0430 AC: 220 AN: 5120

South Asian (SAS) AF: 0.134 AC: 644 AN: 4810

European-Finnish (FIN) AF: 0.0869 AC: 918 AN: 10560

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7670 AN: 67880

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.115 Hom.: 1945

Bravo AF: 0.135

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.31
DANN	Benign	0.74
PhyloP100		-0.12
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: rs1043908; hg19: chr1-230417294;