15-59618352-C-A

Variant names:

• chr15-59618352-C-A
• rs1827358590
• NM_004751.3:c.114C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004751.3(GCNT3):​c.114C>A​(p.Asp38Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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: 31)
• Consequence: GCNT3 NM_004751.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.056639582).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT3	NM_004751.3	c.114C>A	p.Asp38Glu	missense_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.114C>A	p.Asp38Glu	missense_variant	Exon 3 of 3	1	NM_004751.3	ENSP00000379377.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.0060
DANN	Benign	0.73
DEOGEN2	Benign	0.0097	T;T;T;.;.
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.017	N
LIST_S2	Benign	0.48	T;.;T;T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.057	T;T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.46	.;N;N;.;.
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-1.3	N;N;N;D;N
REVEL	Benign	0.026
Sift	Benign	0.32	.;T;T;.;.
Sift4G	Benign	0.28	T;T;T;D;T
Polyphen		0.0	.;B;B;.;.
Vest4		0.030, 0.013
MutPred		0.24		Loss of stability (P = 0.0624);Loss of stability (P = 0.0624);Loss of stability (P = 0.0624);Loss of stability (P = 0.0624);Loss of stability (P = 0.0624);
MVP		0.14
ClinPred		0.28	T
GERP RS		-11
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.043
gMVP		0.31

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: rs1827358590; hg19: chr15-59910551;