Variant 12-122208118-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030765.4(B3GNT4):c.*738dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 658,770 control chromosomes in the GnomAD database, including 1,460 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.055 ( 320 hom., cov: 32)

Exomes 𝑓: 0.062 ( 1140 hom. )

Consequence

B3GNT4
NM_030765.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.238

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 -10 ACMG points.

BP6

Variant 12-122208118-T-TA is Benign according to our data. Variant chr12-122208118-T-TA is described in ClinVar as [Benign]. Clinvar id is 1279245.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DIABLO	NM_001371333.1 linkuse as main transcript	c.262_263insT		3_prime_UTR_variant	6/6	ENST00000464942.7
B3GNT4	NM_030765.4 linkuse as main transcript	c.*738dup		3_prime_UTR_variant	3/3	ENST00000324189.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GNT4	ENST00000324189.5 linkuse as main transcript	c.*738dup		3_prime_UTR_variant	3/3	1	NM_030765.4	A2	Q9C0J1-1
DIABLO	ENST00000464942.7 linkuse as main transcript	c.262_263insT		3_prime_UTR_variant	6/6	1	NM_001371333.1	P1	Q9NR28-1

Frequencies

GnomAD3 genomes

AF:

0.0546

AC:

8286

AN:

151770

Hom.:

320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0202

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0351

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.0231

Gnomad FIN

AF:

0.0642

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0840

Gnomad OTH

AF:

0.0544

GnomAD3 exomes

AF:

0.0512

AC:

6694

AN:

130736

Hom.:

212

AF XY:

0.0518

AC XY:

3695

AN XY:

71326

show subpopulations

Gnomad AFR exome

AF:

0.0188

Gnomad AMR exome

AF:

0.0273

Gnomad ASJ exome

AF:

0.0576

Gnomad EAS exome

AF:

0.000286

Gnomad SAS exome

AF:

0.0292

Gnomad FIN exome

AF:

0.0698

Gnomad NFE exome

AF:

0.0836

Gnomad OTH exome

AF:

0.0604

GnomAD4 exome

AF:

0.0621

AC:

31476

AN:

506882

Hom.:

1140

Cov.:

AF XY:

0.0614

AC XY:

16913

AN XY:

275420

show subpopulations

Gnomad4 AFR exome

AF:

0.0202

Gnomad4 AMR exome

AF:

0.0275

Gnomad4 ASJ exome

AF:

0.0552

Gnomad4 EAS exome

AF:

0.000427

Gnomad4 SAS exome

AF:

0.0283

Gnomad4 FIN exome

AF:

0.0632

Gnomad4 NFE exome

AF:

0.0822

Gnomad4 OTH exome

AF:

0.0553

GnomAD4 genome

AF:

0.0545

AC:

8283

AN:

151888

Hom.:

320

Cov.:

AF XY:

0.0524

AC XY:

3892

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.0201

Gnomad4 AMR

AF:

0.0350

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0233

Gnomad4 FIN

AF:

0.0642

Gnomad4 NFE

AF:

0.0840

Gnomad4 OTH

AF:

0.0538

Bravo

AF:

0.0505

Asia WGS

AF:

0.0180

AC:

AN:

3476

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

Dec 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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