rs2730351

Variant names:

• chr3-16174393-A-G
• rs2730351
• ENST00000961729.1:c.-759A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-16174393-A-G
• chr3-16174393-A-T

Variant summary

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

The ENST00000961729.1(GALNT15):​c.-759A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,142 control chromosomes in the GnomAD database, including 31,839 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 0.64 (31839 hom., cov: 33)
• Consequence: GALNT15 ENST00000961729.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 2 publications found

Genes affected

GALNT15 (HGNC:21531): (polypeptide N-acetylgalactosaminyltransferase 15) Predicted to enable polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in O-glycan processing. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000961729.1. 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
	GALNT15	ENST00000961729.1		c.-759A>G		upstream_gene	N/A	ENSP00000631788.1
	GALNT15	ENST00000961725.1		c.-759A>G		upstream_gene	N/A	ENSP00000631784.1
	GALNT15	ENST00000961726.1		c.-759A>G		upstream_gene	N/A	ENSP00000631785.1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97691 AN: 152024 Hom.: 31817 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.643 AC: 97753 AN: 152142 Hom.: 31839 Cov.: 33 AF XY: 0.643 AC XY: 47849 AN XY: 74372

African (AFR) AF: 0.559 AC: 23199 AN: 41502

American (AMR) AF: 0.606 AC: 9268 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5162

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4822

European-Finnish (FIN) AF: 0.783 AC: 8297 AN: 10594

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47635 AN: 67984

Other (OTH) AF: 0.637 AC: 1346 AN: 2114

Alfa AF: 0.665 Hom.: 14956

Bravo AF: 0.628

Asia WGS AF: 0.521 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.78
PhyloP100		-0.74
PromoterAI		0.084	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2730351; hg19: chr3-16215900;