rs6721582

Positions:

• chr2-165764726-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000392701.8(GALNT3):​c.688+158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,000 control chromosomes in the GnomAD database, including 6,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (6251 hom., cov: 33)
• Consequence: GALNT3 ENST00000392701.8 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0370

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 2-165764726-G-A is Benign according to our data. Variant chr2-165764726-G-A is described in ClinVar as [Benign]. Clinvar id is 1245536.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT3	NM_004482.4	c.688+158C>T		intron_variant		ENST00000392701.8	NP_004473.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT3	ENST00000392701.8	c.688+158C>T		intron_variant		1	NM_004482.4	ENSP00000376465	P1
GALNT3	ENST00000412248.5	c.688+158C>T		intron_variant		5		ENSP00000412643
GALNT3	ENST00000437849.1	c.76+158C>T		intron_variant, NMD_transcript_variant		5		ENSP00000391104

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43094 AN: 151882 Hom.: 6249 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.284 AC: 43118 AN: 152000 Hom.: 6251 Cov.: 33 AF XY: 0.287 AC XY: 21324 AN XY: 74308

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.289

Alfa AF: 0.271 Hom.: 5218

Bravo AF: 0.285

Asia WGS AF: 0.339 AC: 1176 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.2
DANN	Benign	0.69

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: rs6721582; hg19: chr2-166621236;