rs3761944

Variant names:

• chr1-230253243-G-C
• rs3761944
• NM_004481.5:c.1010-1975G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-230253243-G-C
• chr1-230253243-G-T

Variant summary

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

The NM_004481.5(GALNT2):​c.1010-1975G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,966 control chromosomes in the GnomAD database, including 17,762 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 0.47 (17762 hom., cov: 32)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• 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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.1010-1975G>C		intron_variant	Intron 10 of 15	ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.896-1975G>C		intron_variant	Intron 10 of 15		NP_001278795.1
GALNT2	XM_017000964.3	c.917-1975G>C		intron_variant	Intron 11 of 16		XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.1010-1975G>C		intron_variant	Intron 10 of 15	1	NM_004481.5	ENSP00000355632.4

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71975 AN: 151848 Hom.: 17747 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.474 AC: 72036 AN: 151966 Hom.: 17762 Cov.: 32 AF XY: 0.476 AC XY: 35357 AN XY: 74286

African (AFR) AF: 0.570 AC: 23612 AN: 41418

American (AMR) AF: 0.568 AC: 8665 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1501 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3809 AN: 5170

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4111 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26888 AN: 67964

Other (OTH) AF: 0.460 AC: 967 AN: 2104

Alfa AF: 0.423 Hom.: 1706

Bravo AF: 0.497

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.41
PhyloP100		-1.2
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: rs3761944; hg19: chr1-230388989;