15-59619693-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004751.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCNT3	NM_004751.3	MANE Select	c.*138G>T		3_prime_UTR	Exon 3 of 3	NP_004742.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCNT3	ENST00000396065.3	TSL:1 MANE Select	c.*138G>T		3_prime_UTR	Exon 3 of 3	ENSP00000379377.1
	GCNT3	ENST00000560585.5	TSL:1	c.*138G>T		3_prime_UTR	Exon 3 of 3	ENSP00000452741.1
	GCNT3	ENST00000560210.1	TSL:3	n.351+2812G>T		intron	N/A

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

African (AFR) AF: 0.766 AC: 11005 AN: 14360

American (AMR) AF: 0.969 AC: 25631 AN: 26454

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 14301 AN: 14536

East Asian (EAS) AF: 0.703 AC: 24438 AN: 34750

South Asian (SAS) AF: 0.761 AC: 37961 AN: 49868

European-Finnish (FIN) AF: 0.949 AC: 46071 AN: 48560

Middle Eastern (MID) AF: 0.946 AC: 3127 AN: 3306

European-Non Finnish (NFE) AF: 0.964 AC: 294575 AN: 305628

Other (OTH) AF: 0.931 AC: 26538 AN: 28508

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

African (AFR) AF: 0.769 AC: 31879 AN: 41434

American (AMR) AF: 0.955 AC: 14606 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3411 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3810 AN: 5162

South Asian (SAS) AF: 0.747 AC: 3605 AN: 4826

European-Finnish (FIN) AF: 0.945 AC: 10015 AN: 10602

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65459 AN: 68002

Other (OTH) AF: 0.914 AC: 1929 AN: 2110

Alfa AF: 0.941 Hom.: 258994

Bravo AF: 0.895

Asia WGS AF: 0.758 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3743119; hg19: chr15-59911892;