15-59619693-G-T

Variant names:

• chr15-59619693-G-T
• rs3743119
• NM_004751.3:c.*138G>T

Variant summary

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

The NM_004751.3(GCNT3):​c.*138G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 678,068 control chromosomes in the GnomAD database, including 285,891 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 0.89 (61348 hom., cov: 30)
  • Exomes 𝑓: 0.92 (224543 hom.)
• Consequence: GCNT3 NM_004751.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT3	NM_004751.3	c.*138G>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000396065.3	NP_004742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCNT3	ENST00000396065.3	c.*138G>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_004751.3	ENSP00000379377.1
GCNT3	ENST00000560585.5	c.*138G>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000452741.1
GCNT3	ENST00000560210.1	n.351+2812G>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135809 AN: 151980 Hom.: 61322 Cov.: 30

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.917

GnomAD4 exome AF: 0.920 AC: 483647 AN: 525970 Hom.: 224543 Cov.: 5 AF XY: 0.913 AC XY: 254151 AN XY: 278372

Gnomad4 AFR exome AF: 0.766

Gnomad4 AMR exome AF: 0.969

Gnomad4 ASJ exome AF: 0.984

Gnomad4 EAS exome AF: 0.703

Gnomad4 SAS exome AF: 0.761

Gnomad4 FIN exome AF: 0.949

Gnomad4 NFE exome AF: 0.964

Gnomad4 OTH exome AF: 0.931

GnomAD4 genome AF: 0.893 AC: 135885 AN: 152098 Hom.: 61348 Cov.: 30 AF XY: 0.891 AC XY: 66225 AN XY: 74356

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.914

Alfa AF: 0.951 Hom.: 116694

Bravo AF: 0.895

Asia WGS AF: 0.758 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3743119; hg19: chr15-59911892;