15-59602418-C-T

Variant names:

• chr15-59602418-C-T
• rs6494120
• ENST00000559189.5:c.-465+2707C>T

Variant summary

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

The ENST00000559189.5(GCNT3):​c.-465+2707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,084 control chromosomes in the GnomAD database, including 28,040 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 0.59 (28040 hom., cov: 33)
• Consequence: GCNT3 ENST00000559189.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 5 publications found

Genes affected

GCNT3 (HGNC:4205): (glucosaminyl (N-acetyl) transferase 3, mucin type) This gene encodes a member of the N-acetylglucosaminyltransferase family. The encoded protein is a beta-6-N-acetylglucosamine-transferase that catalyzes the formation of core 2 and core 4 O-glycans on mucin-type glycoproteins.[provided by RefSeq, Apr 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 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
GCNT3	ENST00000559189.5	c.-465+2707C>T		intron_variant	Intron 1 of 4	3		ENSP00000453453.1
GCNT3	ENST00000558721.5	n.101+6064C>T		intron_variant	Intron 2 of 5	4
GCNT3	ENST00000560111.5	n.59+2707C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89221 AN: 151966 Hom.: 27984 Cov.: 33

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.587 AC: 89332 AN: 152084 Hom.: 28040 Cov.: 33 AF XY: 0.593 AC XY: 44123 AN XY: 74356

African (AFR) AF: 0.808 AC: 33522 AN: 41502

American (AMR) AF: 0.449 AC: 6871 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1603 AN: 3456

East Asian (EAS) AF: 0.705 AC: 3650 AN: 5176

South Asian (SAS) AF: 0.743 AC: 3586 AN: 4826

European-Finnish (FIN) AF: 0.633 AC: 6687 AN: 10562

Middle Eastern (MID) AF: 0.579 AC: 168 AN: 290

European-Non Finnish (NFE) AF: 0.466 AC: 31639 AN: 67964

Other (OTH) AF: 0.526 AC: 1113 AN: 2114

Alfa AF: 0.502 Hom.: 63024

Bravo AF: 0.581

Asia WGS AF: 0.716 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.55
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs6494120; hg19: chr15-59894617;