chr15-59620054-A-C

Position:

• chr15-59620054-A-C

Variant summary

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

The NM_004751.3(GCNT3):​c.*499A>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 0.912 in 169,298 control chromosomes in the GnomAD database, including 70,833 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 0.91 (63088 hom., cov: 32)
  • Exomes 𝑓: 0.95 (7745 hom.)
• Consequence: GCNT3 NM_004751.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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]

GCNT3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GCNT3	NM_004751.3	c.*499A>C		3_prime_UTR_variant	3/3	ENST00000396065.3	NP_004742.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCNT3	ENST00000396065.3	c.*499A>C		3_prime_UTR_variant	3/3	1	NM_004751.3	ENSP00000379377.1
GCNT3	ENST00000560210.1	n.351+3173A>C		intron_variant		3
GCNT3	ENST00000560585.5	c.*499A>C		downstream_gene_variant		1		ENSP00000452741.1

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138005 AN: 152092 Hom.: 63059 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.928

GnomAD4 exome AF: 0.951 AC: 16258 AN: 17088 Hom.: 7745 Cov.: 0 AF XY: 0.951 AC XY: 7798 AN XY: 8196

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.973

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.688

Gnomad4 SAS exome AF: 0.727

Gnomad4 FIN exome AF: 0.951

Gnomad4 NFE exome AF: 0.967

Gnomad4 OTH exome AF: 0.958

GnomAD4 genome AF: 0.907 AC: 138092 AN: 152210 Hom.: 63088 Cov.: 32 AF XY: 0.904 AC XY: 67235 AN XY: 74410

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.926

Alfa AF: 0.929 Hom.: 16622

Bravo AF: 0.910

Asia WGS AF: 0.776 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7181069; hg19: chr15-59912253;