rs10771515
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000539757.1(DDX12B):n.2325T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 26)
Exomes 𝑓: 0.0000024 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DDX12B
ENST00000539757.1 non_coding_transcript_exon
ENST00000539757.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.58
Publications
8 publications found
Genes affected
DDX12B (HGNC:38668): (DEAD/H-box helicase 12B%2C pseudogene [Source:HGNC Symbol%3BAcc:HGNC:38668])
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=-0.53).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LOC642846 | NR_024374.1 | n.2435T>A | non_coding_transcript_exon_variant | Exon 21 of 22 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DDX12B | ENST00000539757.1 | n.2325T>A | non_coding_transcript_exon_variant | Exon 22 of 29 | 6 | |||||
| ENSG00000299001 | ENST00000759736.1 | n.139+1831A>T | intron_variant | Intron 1 of 1 | ||||||
| ENSG00000299001 | ENST00000759737.1 | n.108+1831A>T | intron_variant | Intron 1 of 2 | ||||||
| ENSG00000299001 | ENST00000759738.1 | n.165-1747A>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
26
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000238 AC: 3AN: 1261208Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 637268 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
1261208
Hom.:
Cov.:
20
AF XY:
AC XY:
0
AN XY:
637268
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:
30272
American (AMR)
AF:
AC:
0
AN:
44230
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24708
East Asian (EAS)
AF:
AC:
0
AN:
38806
South Asian (SAS)
AF:
AC:
0
AN:
82390
European-Finnish (FIN)
AF:
AC:
0
AN:
53142
Middle Eastern (MID)
AF:
AC:
0
AN:
5306
European-Non Finnish (NFE)
AF:
AC:
2
AN:
928642
Other (OTH)
AF:
AC:
0
AN:
53712
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0245704), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.358
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
26
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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