chr12-122208273-T-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000342392.3(DIABLO):n.*658A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000222 in 1,352,408 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 8.3e-7 ( 0 hom. )
Consequence
DIABLO
ENST00000342392.3 non_coding_transcript_exon
ENST00000342392.3 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.220
Publications
31 publications found
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]
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| B3GNT4 | NM_030765.4 | c.*885T>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000324189.5 | NP_110392.1 | ||
| DIABLO | NM_001371333.1 | c.*108A>T | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000464942.7 | NP_001358262.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000256861 | ENST00000535844.1 | n.*622A>T | non_coding_transcript_exon_variant | Exon 16 of 16 | 2 | ENSP00000454454.1 | ||||
| B3GNT4 | ENST00000324189.5 | c.*885T>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_030765.4 | ENSP00000319636.4 | |||
| DIABLO | ENST00000464942.7 | c.*108A>T | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_001371333.1 | ENSP00000442360.2 | |||
| ENSG00000256861 | ENST00000535844.1 | n.*622A>T | 3_prime_UTR_variant | Exon 16 of 16 | 2 | ENSP00000454454.1 |
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
151958
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00000482 AC: 1AN: 207302 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
207302
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 8.33e-7 AC: 1AN: 1200450Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 606962 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1200450
Hom.:
Cov.:
17
AF XY:
AC XY:
0
AN XY:
606962
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
28120
American (AMR)
AF:
AC:
0
AN:
41364
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24266
East Asian (EAS)
AF:
AC:
0
AN:
37910
South Asian (SAS)
AF:
AC:
0
AN:
79700
European-Finnish (FIN)
AF:
AC:
0
AN:
39482
Middle Eastern (MID)
AF:
AC:
0
AN:
3692
European-Non Finnish (NFE)
AF:
AC:
0
AN:
893970
Other (OTH)
AF:
AC:
0
AN:
51946
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000132 AC: 2AN: 151958Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74210 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
151958
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74210
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41400
American (AMR)
AF:
AC:
0
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5152
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10574
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67954
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.600
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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