Variant 12-122208327-A-G 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 NM_030765.4(B3GNT4):c.*939A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0413 in 1,597,692 control chromosomes in the GnomAD database, including 12,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 6226 hom., cov: 32)

Exomes 𝑓: 0.028 ( 5958 hom. )

Consequence

B3GNT4
NM_030765.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.71

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=-0.91).

BP6

Variant 12-122208327-A-G is Benign according to our data. Variant chr12-122208327-A-G is described in ClinVar as [Benign]. Clinvar id is 1249498.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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.*54T>C		3_prime_UTR_variant	6/6	ENST00000464942.7	NP_001358262.1
B3GNT4	NM_030765.4 linkuse as main transcript	c.*939A>G		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.*939A>G		3_prime_UTR_variant	3/3	1	NM_030765.4	ENSP00000319636	A2	Q9C0J1-1
DIABLO	ENST00000464942.7 linkuse as main transcript	c.*54T>C		3_prime_UTR_variant	6/6	1	NM_001371333.1	ENSP00000442360	P1	Q9NR28-1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

25007

AN:

152070

Hom.:

6207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0654

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.0482

Gnomad SAS

AF:

0.0719

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.116

GnomAD3 exomes

AF:

0.0586

AC:

14358

AN:

244920

Hom.:

2528

AF XY:

0.0503

AC XY:

6693

AN XY:

132980

show subpopulations

Gnomad AFR exome

AF:

0.547

Gnomad AMR exome

AF:

0.0315

Gnomad ASJ exome

AF:

0.0398

Gnomad EAS exome

AF:

0.0472

Gnomad SAS exome

AF:

0.0620

Gnomad FIN exome

AF:

0.00414

Gnomad NFE exome

AF:

0.0105

Gnomad OTH exome

AF:

0.0357

GnomAD4 exome

AF:

0.0283

AC:

40846

AN:

1445504

Hom.:

5958

Cov.:

AF XY:

0.0276

AC XY:

19886

AN XY:

719928

show subpopulations

Gnomad4 AFR exome

AF:

0.566

Gnomad4 AMR exome

AF:

0.0351

Gnomad4 ASJ exome

AF:

0.0415

Gnomad4 EAS exome

AF:

0.0375

Gnomad4 SAS exome

AF:

0.0613

Gnomad4 FIN exome

AF:

0.00411

Gnomad4 NFE exome

AF:

0.00826

Gnomad4 OTH exome

AF:

0.0529

GnomAD4 genome

AF:

0.165

AC:

25068

AN:

152188

Hom.:

6226

Cov.:

AF XY:

0.160

AC XY:

11924

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.538

Gnomad4 AMR

AF:

0.0654

Gnomad4 ASJ

AF:

0.0421

Gnomad4 EAS

AF:

0.0487

Gnomad4 SAS

AF:

0.0717

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.0512

Hom.:

991

Bravo

AF:

0.186

Asia WGS

AF:

0.0910

AC:

315

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 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.028

DANN

Benign

0.24

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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