chr9-76423254-T-G

Position:

• chr9-76423254-T-G

Variant summary

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

The NM_001407181.1(GCNT1):​c.-744-18607T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,136 control chromosomes in the GnomAD database, including 6,910 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 0.30 (6910 hom., cov: 33)
• Consequence: GCNT1 NM_001407181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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]

GCNT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GCNT1	NM_001407181.1	c.-744-18607T>G		intron_variant			NP_001394110.1
GCNT1	NM_001407182.1	c.-290+27683T>G		intron_variant			NP_001394111.1
GCNT1	NM_001407183.1	c.-290+28834T>G		intron_variant			NP_001394112.1
GCNT1	NM_001407184.1	c.-290+27683T>G		intron_variant			NP_001394113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCNT1	ENST00000488136.5	n.38+3367T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45148 AN: 152018 Hom.: 6903 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.297 AC: 45181 AN: 152136 Hom.: 6910 Cov.: 33 AF XY: 0.296 AC XY: 22031 AN XY: 74366

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.323

Alfa AF: 0.187 Hom.: 509

Bravo AF: 0.305

Asia WGS AF: 0.313 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6560517; hg19: chr9-79038170;