rs28404113

Variant names:

• chr1-230067361-C-A
• rs28404113
• NM_004481.5:c.81C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-230067361-C-A
• chr1-230067361-C-G
• chr1-230067361-C-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_004481.5(GALNT2):​c.81C>A​(p.Gly27Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G27G) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GALNT2 NM_004481.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 1 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP7: Synonymous conserved (PhyloP=1.53 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.81C>A	p.Gly27Gly	synonymous_variant	Exon 1 of 16	ENST00000366672.5	NP_004472.1
GALNT2	NR_120373.2	n.124C>A		non_coding_transcript_exon_variant	Exon 1 of 2
GALNT2	NM_001291866.2	c.12+9283C>A		intron_variant	Intron 1 of 15		NP_001278795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.81C>A	p.Gly27Gly	synonymous_variant	Exon 1 of 16	1	NM_004481.5	ENSP00000355632.4
GALNT2	ENST00000488903.1	n.103C>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
GALNT2	ENST00000494106.1	n.89+9283C>A		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1204082 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 592168

African (AFR) AF: 0.00 AC: 0 AN: 24186

American (AMR) AF: 0.00 AC: 0 AN: 19588

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18406

East Asian (EAS) AF: 0.00 AC: 0 AN: 25186

South Asian (SAS) AF: 0.00 AC: 0 AN: 51620

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4226

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 974654

Other (OTH) AF: 0.00 AC: 0 AN: 46612

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.88
PhyloP100		1.5
PromoterAI		0.072	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.9
Mutation Taster		=300/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs28404113; hg19: chr1-230203108;