15-59602418-C-T

Position:

• chr15-59602418-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GCNT3	XM_047433341.1	c.-465+2707C>T		intron_variant			XP_047289297.1
GCNT3	XM_047433342.1	c.-465+6064C>T		intron_variant			XP_047289298.1
GCNT3	XM_047433343.1	c.-464-7317C>T		intron_variant			XP_047289299.1
GCNT3	XM_047433344.1	c.-464-7317C>T		intron_variant			XP_047289300.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCNT3	ENST00000559189.5	c.-465+2707C>T		intron_variant		3		ENSP00000453453
GCNT3	ENST00000558721.5	n.101+6064C>T		intron_variant, non_coding_transcript_variant		4
GCNT3	ENST00000560111.5	n.59+2707C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.526

Alfa AF: 0.483 Hom.: 37724

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494120; hg19: chr15-59894617;