Variant chr12-122208273-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000324189.5(B3GNT4):c.*885T>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 0.598 in 1,350,324 control chromosomes in the GnomAD database, including 245,794 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 34823 hom., cov: 31)

Exomes 𝑓: 0.59 ( 210971 hom. )

Consequence

B3GNT4
ENST00000324189.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.220

Variant links:

Genes affected

DIABLO (HGNC:21528): (diablo IAP-binding mitochondrial protein) This gene encodes an inhibitor of apoptosis protein (IAP)-binding protein. The encoded mitochondrial protein enters the cytosol when cells undergo apoptosis, and allows activation of caspases by binding to inhibitor of apoptosis proteins. Overexpression of the encoded protein sensitizes tumor cells to apoptosis. A mutation in this gene is associated with young-adult onset of nonsyndromic deafness-64. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

DIABLO links:

B3GNT4 (HGNC:15683): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase protein family. The encoded enzyme is involved in the biosynthesis of poly-N-acetyllactosamine chains and prefers lacto-N-neotetraose as a substrate. It is a type II transmembrane protein. [provided by RefSeq, Jul 2008]

B3GNT4 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 12-122208273-T-C is Benign according to our data. Variant chr12-122208273-T-C is described in ClinVar as [Benign]. Clinvar id is 1247587.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIABLO	NM_001371333.1 linkuse as main transcript	c.*108A>G		3_prime_UTR_variant	6/6	ENST00000464942.7	NP_001358262.1
B3GNT4	NM_030765.4 linkuse as main transcript	c.*885T>C		3_prime_UTR_variant	3/3	ENST00000324189.5	NP_110392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GNT4	ENST00000324189.5 linkuse as main transcript	c.*885T>C		3_prime_UTR_variant	3/3	1	NM_030765.4	ENSP00000319636	A2	Q9C0J1-1
DIABLO	ENST00000464942.7 linkuse as main transcript	c.*108A>G		3_prime_UTR_variant	6/6	1	NM_001371333.1	ENSP00000442360	P1	Q9NR28-1

Frequencies

GnomAD3 genomes

AF:

0.660

AC:

100217

AN:

151898

Hom.:

34782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.881

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.592

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.629

GnomAD3 exomes

AF:

0.605

AC:

125475

AN:

207302

Hom.:

38819

AF XY:

0.602

AC XY:

68251

AN XY:

113462

show subpopulations

Gnomad AFR exome

AF:

0.890

Gnomad AMR exome

AF:

0.545

Gnomad ASJ exome

AF:

0.576

Gnomad EAS exome

AF:

0.797

Gnomad SAS exome

AF:

0.593

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.573

Gnomad OTH exome

AF:

0.563

GnomAD4 exome

AF:

0.590

AC:

706790

AN:

1198308

Hom.:

210971

Cov.:

AF XY:

0.588

AC XY:

356487

AN XY:

605958

show subpopulations

Gnomad4 AFR exome

AF:

0.895

Gnomad4 AMR exome

AF:

0.547

Gnomad4 ASJ exome

AF:

0.571

Gnomad4 EAS exome

AF:

0.767

Gnomad4 SAS exome

AF:

0.592

Gnomad4 FIN exome

AF:

0.509

Gnomad4 NFE exome

AF:

0.578

Gnomad4 OTH exome

AF:

0.602

GnomAD4 genome

AF:

0.660

AC:

100319

AN:

152016

Hom.:

34823

Cov.:

AF XY:

0.655

AC XY:

48696

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.576

Gnomad4 EAS

AF:

0.796

Gnomad4 SAS

AF:

0.592

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.570

Gnomad4 OTH

AF:

0.628

Alfa

AF:

0.578

Hom.:

37363

Bravo

AF:

0.677

Asia WGS

AF:

0.670

AC:

2326

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 22, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.1

DANN

Benign

0.48

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

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