rs1886268

Variant names:

• chr9-76541853-C-T
• rs1886268
• ENST00000648797.1:n.626+13958C>T

Variant summary

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

The ENST00000648797.1(GCNT1):​n.626+13958C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,080 control chromosomes in the GnomAD database, including 5,584 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 0.23 (5584 hom., cov: 32)
• Consequence: GCNT1 ENST00000648797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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.626+13958C>T		intron_variant	Intron 5 of 12

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34613 AN: 151962 Hom.: 5577 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.228 AC: 34664 AN: 152080 Hom.: 5584 Cov.: 32 AF XY: 0.227 AC XY: 16850 AN XY: 74372

African (AFR) AF: 0.436 AC: 18077 AN: 41440

American (AMR) AF: 0.218 AC: 3330 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 792 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4826

European-Finnish (FIN) AF: 0.0837 AC: 887 AN: 10600

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8176 AN: 67990

Other (OTH) AF: 0.221 AC: 466 AN: 2110

Alfa AF: 0.159 Hom.: 11099

Bravo AF: 0.249

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.26
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1886268; hg19: chr9-79156769;