rs664832

Variant names:

• chr9-76493454-A-G
• rs664832
• NM_001490.5:c.-289-7462A>G

Variant summary

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

The NM_001490.5(GCNT1):​c.-289-7462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,984 control chromosomes in the GnomAD database, including 7,632 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 0.31 (7632 hom., cov: 32)
• Consequence: GCNT1 NM_001490.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT1	NM_001490.5	c.-289-7462A>G		intron_variant	Intron 2 of 3	ENST00000376730.5	NP_001481.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCNT1	ENST00000376730.5	c.-289-7462A>G		intron_variant	Intron 2 of 3	1	NM_001490.5	ENSP00000365920.4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46990 AN: 151866 Hom.: 7630 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.309 AC: 47025 AN: 151984 Hom.: 7632 Cov.: 32 AF XY: 0.304 AC XY: 22603 AN XY: 74298

African (AFR) AF: 0.395 AC: 16364 AN: 41418

American (AMR) AF: 0.245 AC: 3742 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5172

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2709 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20073 AN: 67940

Other (OTH) AF: 0.333 AC: 703 AN: 2108

Alfa AF: 0.290 Hom.: 785

Bravo AF: 0.311

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs664832; hg19: chr9-79108370;