dbSNP rs7181069: GCNT3:c.*499A>C (chr15-59620054-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

Publications

3 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT3	NM_004751.3 link	c.*499A>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000396065.3	NP_004742.1	O95395A0A024R5T9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GCNT3	ENST00000396065.3 link	c.*499A>C	3_prime_UTR_variant	Exon 3 of 3	1	NM_004751.3	ENSP00000379377.1	O95395
GCNT3	ENST00000560210.1 link	n.351+3173A>C	intron_variant	Intron 1 of 1	3
GCNT3	ENST00000560585.5 link	c.*499A>C	downstream_gene_variant		1		ENSP00000452741.1	O95395

Frequencies

GnomAD3 genomes

AF:

0.907

AC:

138005

AN:

152092

Hom.:

63059

Cov.:

show subpopulations

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.:

AF XY:

0.951

AC XY:

7798

AN XY:

8196

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.973

AC:

469

AN:

482

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.688

AC:

AN:

South Asian (SAS)

AF:

0.727

AC:

AN:

110

European-Finnish (FIN)

AF:

0.951

AC:

13998

AN:

14716

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.967

AC:

1516

AN:

1568

Other (OTH)

AF:

0.958

AC:

159

AN:

166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

116

155

194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.907

AC:

138092

AN:

152210

Hom.:

63088

Cov.:

AF XY:

0.904

AC XY:

67235

AN XY:

74410

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

608

1217

1825

2434

3042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.51

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over