chr9-76545077-G-T

Position:

• chr9-76545077-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648797.1(GCNT1):​n.626+17182G>T 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 0.328 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.76).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCNT1	ENST00000648797.1	n.626+17182G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.325

Alfa AF: 0.370 Hom.: 10803

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927632; hg19: chr9-79159993;