Variant chr6-10528886-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_145649.5(GCNT2):c.-26A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 1,539,366 control chromosomes in the GnomAD database, including 5,049 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.057 ( 370 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4679 hom. )

Consequence

GCNT2
NM_145649.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0690

Variant links:

Genes affected

GCNT2 (HGNC:4204): (glucosaminyl (N-acetyl) transferase 2 (I blood group)) This gene encodes the enzyme responsible for formation of the blood group I antigen. The i and I antigens are distinguished by linear and branched poly-N-acetyllactosaminoglycans, respectively. The encoded protein is the I-branching enzyme, a beta-1,6-N-acetylglucosaminyltransferase responsible for the conversion of fetal i antigen to adult I antigen in erythrocytes during embryonic development. Mutations in this gene have been associated with adult i blood group phenotype. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

GCNT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 6-10528886-A-C is Benign according to our data. Variant chr6-10528886-A-C is described in ClinVar as [Benign]. Clinvar id is 1285739.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GCNT2	NM_145649.5 linkuse as main transcript	c.-26A>C		5_prime_UTR_variant	3/5	ENST00000495262.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCNT2	ENST00000495262.7 linkuse as main transcript	c.-26A>C		5_prime_UTR_variant	3/5	2	NM_145649.5	P3	Q8N0V5-1

Frequencies

GnomAD3 genomes

AF:

0.0573

AC:

8724

AN:

152140

Hom.:

370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0685

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0232

Gnomad FIN

AF:

0.0333

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0852

Gnomad OTH

AF:

0.0789

GnomAD3 exomes

AF:

0.0582

AC:

14605

AN:

251022

Hom.:

616

AF XY:

0.0594

AC XY:

8063

AN XY:

135818

show subpopulations

Gnomad AFR exome

AF:

0.0163

Gnomad AMR exome

AF:

0.0464

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.0240

Gnomad FIN exome

AF:

0.0361

Gnomad NFE exome

AF:

0.0841

Gnomad OTH exome

AF:

0.0731

GnomAD4 exome

AF:

0.0757

AC:

105007

AN:

1387108

Hom.:

4679

Cov.:

AF XY:

0.0747

AC XY:

51891

AN XY:

694592

show subpopulations

Gnomad4 AFR exome

AF:

0.0125

Gnomad4 AMR exome

AF:

0.0490

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.000153

Gnomad4 SAS exome

AF:

0.0237

Gnomad4 FIN exome

AF:

0.0367

Gnomad4 NFE exome

AF:

0.0870

Gnomad4 OTH exome

AF:

0.0724

GnomAD4 genome

AF:

0.0573

AC:

8719

AN:

152258

Hom.:

370

Cov.:

AF XY:

0.0536

AC XY:

3988

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0175

Gnomad4 AMR

AF:

0.0684

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0228

Gnomad4 FIN

AF:

0.0333

Gnomad4 NFE

AF:

0.0852

Gnomad4 OTH

AF:

0.0781

Alfa

AF:

0.0531

Hom.:

Bravo

AF:

0.0594

Asia WGS

AF:

0.00866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.0

DANN

Benign

0.50

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over