2-165832832-T-C

Variant names:

• chr2-165832832-T-C
• rs2060167
• ENST00000715282.1:c.-109+13121A>G

Variant summary

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

The ENST00000715282.1(GALNT3):​c.-109+13121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,732 control chromosomes in the GnomAD database, including 35,928 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 0.68 (35928 hom., cov: 29)
• Consequence: GALNT3 ENST00000715282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 5 publications found

Genes affected

GALNT3 (HGNC:4125): (polypeptide N-acetylgalactosaminyltransferase 3) This gene encodes UDP-GalNAc transferase 3, a member of the GalNAc-transferases family. This family transfers an N-acetyl galactosamine to the hydroxyl group of a serine or threonine residue in the first step of O-linked oligosaccharide biosynthesis. Individual GalNAc-transferases have distinct activities and initiation of O-glycosylation is regulated by a repertoire of GalNAc-transferases. The protein encoded by this gene is highly homologous to other family members, however the enzymes have different substrate specificities. [provided by RefSeq, Jul 2008]

GALNT3 Gene-Disease associations (from GenCC):

• tumoral calcinosis, hyperphosphatemic, familial, 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, G2P
• tumoral calcinosis, hyperphosphatemic, familial, 1

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp

ENSG00000229195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715282.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT3	ENST00000715282.1		c.-109+13121A>G		intron	N/A	ENSP00000520447.1	Q14435-1
	ENSG00000229195	ENST00000428888.1	TSL:5	n.139+13121A>G		intron	N/A
	ENSG00000235192	ENST00000741716.1		n.317-7858T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103265 AN: 151616 Hom.: 35912 Cov.: 29

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.681 AC: 103323 AN: 151732 Hom.: 35928 Cov.: 29 AF XY: 0.680 AC XY: 50373 AN XY: 74130

African (AFR) AF: 0.527 AC: 21778 AN: 41300

American (AMR) AF: 0.710 AC: 10828 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2354 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2903 AN: 5148

South Asian (SAS) AF: 0.732 AC: 3510 AN: 4792

European-Finnish (FIN) AF: 0.757 AC: 7963 AN: 10518

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51532 AN: 67954

Other (OTH) AF: 0.698 AC: 1470 AN: 2106

Alfa AF: 0.736 Hom.: 68017

Bravo AF: 0.670

Asia WGS AF: 0.653 AC: 2270 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.2
DANN	Benign	0.43
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2060167;

hg19: chr2-166689342;