rs3743119

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-59619693-G-C
• chr15-59619693-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004751.3(GCNT3):​c.*138G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000038 in 526,198 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0000038 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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>C		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>C		3_prime_UTR	Exon 3 of 3	ENSP00000379377.1
	GCNT3	ENST00000560585.5	TSL:1	c.*138G>C		3_prime_UTR	Exon 3 of 3	ENSP00000452741.1
	GCNT3	ENST00000560210.1	TSL:3	n.351+2812G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000380 AC: 2 AN: 526198 Hom.: 0 Cov.: 5 AF XY: 0.00000359 AC XY: 1 AN XY: 278496

African (AFR) AF: 0.00 AC: 0 AN: 14376

American (AMR) AF: 0.00 AC: 0 AN: 26456

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14536

East Asian (EAS) AF: 0.00 AC: 0 AN: 34788

South Asian (SAS) AF: 0.00 AC: 0 AN: 49968

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3308

European-Non Finnish (NFE) AF: 0.00000654 AC: 2 AN: 305678

Other (OTH) AF: 0.00 AC: 0 AN: 28514

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 258994

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		0.29

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;