rs2149589

Variant names:

• chr9-76586158-A-G
• rs2149589
• ENST00000648797.1:n.989-19692A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648797.1(GCNT1):​n.989-19692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,050 control chromosomes in the GnomAD database, including 23,574 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 0.55 (23574 hom., cov: 32)
• Consequence: GCNT1 ENST00000648797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

Genes affected

GCNT1 (HGNC:4203): (glucosaminyl (N-acetyl) transferase 1) This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCNT1	ENST00000648797.1	n.989-19692A>G		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83884 AN: 151930 Hom.: 23541 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.552 AC: 83958 AN: 152050 Hom.: 23574 Cov.: 32 AF XY: 0.547 AC XY: 40652 AN XY: 74330

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.534

Alfa AF: 0.552 Hom.: 31806

Bravo AF: 0.548

Asia WGS AF: 0.493 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149589; hg19: chr9-79201074; COSMIC: COSV60362515;