rs2149589

chr9-76586158-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCNT1	ENST00000648797.1	n.989-19692A>G		intron_variant, non_coding_transcript_variant

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;