chr9-76545077-G-T

Variant names:

• chr9-76545077-G-T
• rs927632
• ENST00000648797.1:n.626+17182G>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+17182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,990 control chromosomes in the GnomAD database, including 8,891 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 0.33 (8891 hom., cov: 32)
• Consequence: GCNT1 ENST00000648797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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+17182G>T		intron_variant	Intron 5 of 12

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49914 AN: 151872 Hom.: 8894 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.328 AC: 49927 AN: 151990 Hom.: 8891 Cov.: 32 AF XY: 0.327 AC XY: 24311 AN XY: 74280

African (AFR) AF: 0.242 AC: 10042 AN: 41484

American (AMR) AF: 0.280 AC: 4278 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1406 AN: 3464

East Asian (EAS) AF: 0.189 AC: 976 AN: 5172

South Asian (SAS) AF: 0.239 AC: 1155 AN: 4832

European-Finnish (FIN) AF: 0.431 AC: 4540 AN: 10544

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26457 AN: 67928

Other (OTH) AF: 0.325 AC: 683 AN: 2102

Alfa AF: 0.362 Hom.: 13502

Bravo AF: 0.316

Asia WGS AF: 0.185 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.56
DANN	Benign	0.76
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs927632; hg19: chr9-79159993;