rs7181069

Variant names:

• chr15-59620054-A-C
• rs7181069
• NM_004751.3:c.*499A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCNT3	NM_004751.3	MANE Select	c.*499A>C		3_prime_UTR	Exon 3 of 3	NP_004742.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCNT3	ENST00000396065.3	TSL:1 MANE Select	c.*499A>C		3_prime_UTR	Exon 3 of 3	ENSP00000379377.1
	GCNT3	ENST00000953238.1		c.*499A>C		3_prime_UTR	Exon 4 of 4	ENSP00000623297.1
	GCNT3	ENST00000953239.1		c.*499A>C		3_prime_UTR	Exon 3 of 3	ENSP00000623298.1

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

African (AFR) AF: 1.00 AC: 10 AN: 10

American (AMR) AF: 0.973 AC: 469 AN: 482

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.688 AC: 22 AN: 32

South Asian (SAS) AF: 0.727 AC: 80 AN: 110

European-Finnish (FIN) AF: 0.951 AC: 13998 AN: 14716

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.967 AC: 1516 AN: 1568

Other (OTH) AF: 0.958 AC: 159 AN: 166

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

African (AFR) AF: 0.814 AC: 33766 AN: 41498

American (AMR) AF: 0.958 AC: 14663 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3417 AN: 3472

East Asian (EAS) AF: 0.766 AC: 3960 AN: 5172

South Asian (SAS) AF: 0.751 AC: 3612 AN: 4812

European-Finnish (FIN) AF: 0.945 AC: 10026 AN: 10608

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

European-Non Finnish (NFE) AF: 0.963 AC: 65518 AN: 68028

Other (OTH) AF: 0.926 AC: 1959 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.51
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7181069; hg19: chr15-59912253;