rs2760537

Positions:

• chr1-230190666-G-A
• chr1-230190666-G-T

Variant summary

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

The NM_004481.5(GALNT2):​c.220+12355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,798 control chromosomes in the GnomAD database, including 4,715 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 0.23 (4715 hom., cov: 31)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.220+12355G>A		intron_variant		ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.106+12355G>A		intron_variant			NP_001278795.1
GALNT2	XM_017000964.3	c.127+12355G>A		intron_variant			XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.220+12355G>A		intron_variant		1	NM_004481.5	ENSP00000355632	P1
GALNT2	ENST00000494106.1	n.183+12355G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34143 AN: 151680 Hom.: 4711 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.225 AC: 34167 AN: 151798 Hom.: 4715 Cov.: 31 AF XY: 0.225 AC XY: 16722 AN XY: 74182

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.195

Alfa AF: 0.117 Hom.: 278

Bravo AF: 0.231

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.46

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: rs2760537; hg19: chr1-230326412;