rs2149589

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648797.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCNT1	ENST00000648797.1		n.989-19692A>G		intron	N/A

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

African (AFR) AF: 0.627 AC: 25994 AN: 41458

American (AMR) AF: 0.451 AC: 6893 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2319 AN: 5170

South Asian (SAS) AF: 0.512 AC: 2465 AN: 4818

European-Finnish (FIN) AF: 0.501 AC: 5290 AN: 10568

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37216 AN: 67962

Other (OTH) AF: 0.534 AC: 1130 AN: 2116

Alfa AF: 0.551 Hom.: 43122

Bravo AF: 0.548

Asia WGS AF: 0.493 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.53
PhyloP100		-3.0

Splicing

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

Other links and lift over

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