rs10779835

Variant names:

• chr1-230164203-T-C
• rs10779835
• NM_004481.5:c.127-14015T>C

Variant summary

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

The NM_004481.5(GALNT2):​c.127-14015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,078 control chromosomes in the GnomAD database, including 18,917 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 0.45 (18917 hom., cov: 33)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 16 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.127-14015T>C		intron_variant	Intron 1 of 15	ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.13-14015T>C		intron_variant	Intron 1 of 15		NP_001278795.1
GALNT2	XM_017000964.3	c.34-14015T>C		intron_variant	Intron 2 of 16		XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.127-14015T>C		intron_variant	Intron 1 of 15	1	NM_004481.5	ENSP00000355632.4
GALNT2	ENST00000494106.1	n.90-14015T>C		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69167 AN: 151960 Hom.: 18909 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.455 AC: 69180 AN: 152078 Hom.: 18917 Cov.: 33 AF XY: 0.452 AC XY: 33600 AN XY: 74338

African (AFR) AF: 0.139 AC: 5754 AN: 41504

American (AMR) AF: 0.555 AC: 8489 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3466

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5166

South Asian (SAS) AF: 0.428 AC: 2057 AN: 4810

European-Finnish (FIN) AF: 0.563 AC: 5943 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41668 AN: 67950

Other (OTH) AF: 0.511 AC: 1081 AN: 2114

Alfa AF: 0.548 Hom.: 36890

Bravo AF: 0.441

Asia WGS AF: 0.346 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		-0.49
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: rs10779835; hg19: chr1-230299949;