rs886044938
Your query was ambiguous. Multiple possible variants found:
- chr1-100187700-ATTTTTTT-A
- chr1-100187700-ATTTTTTT-ATT
- chr1-100187700-ATTTTTTT-ATTT
- chr1-100187700-ATTTTTTT-ATTTT
- chr1-100187700-ATTTTTTT-ATTTTT
- chr1-100187700-ATTTTTTT-ATTTTTT
- chr1-100187700-ATTTTTTT-ATTTTTTTT
- chr1-100187700-ATTTTTTT-ATTTTTTTTT
- chr1-100187700-ATTTTTTT-ATTTTTTTTTTTT
- chr1-100187700-ATTTTTTT-ATTTTTTTTTTTTT
- chr1-100187700-ATTTTTTT-ATTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001918.5(DBT):c.*8548_*8554delAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 124,174 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000032 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
DBT
NM_001918.5 3_prime_UTR
NM_001918.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.412
Publications
0 publications found
Genes affected
DBT (HGNC:2698): (dihydrolipoamide branched chain transacylase E2) The branched-chain alpha-keto acid dehydrogenase complex (BCKD) is an inner-mitochondrial enzyme complex involved in the breakdown of the branched-chain amino acids isoleucine, leucine, and valine. The BCKD complex is thought to be composed of a core of 24 transacylase (E2) subunits, and associated decarboxylase (E1), dehydrogenase (E3), and regulatory subunits. This gene encodes the transacylase (E2) subunit. Mutations in this gene result in maple syrup urine disease, type 2. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
DBT Gene-Disease associations (from GenCC):
- maple syrup urine diseaseInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
- maple syrup urine disease type 2Inheritance: AR Classification: DEFINITIVE Submitted by: G2P, Myriad Women’s Health
- classic maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- intermediate maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- intermittent maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- thiamine-responsive maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001918.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DBT | NM_001918.5 | MANE Select | c.*8548_*8554delAAAAAAA | 3_prime_UTR | Exon 11 of 11 | NP_001909.4 | P11182 | ||
| DBT | NM_001399969.1 | c.*8548_*8554delAAAAAAA | 3_prime_UTR | Exon 12 of 12 | NP_001386898.1 | A0A7P0T9W1 | |||
| DBT | NM_001399972.1 | c.*8548_*8554delAAAAAAA | 3_prime_UTR | Exon 12 of 12 | NP_001386901.1 | A0A7P0T9W1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DBT | ENST00000370132.8 | TSL:1 MANE Select | c.*8548_*8554delAAAAAAA | 3_prime_UTR | Exon 11 of 11 | ENSP00000359151.3 | P11182 | ||
| DBT | ENST00000875462.1 | c.*42-4580_*42-4574delAAAAAAA | intron | N/A | ENSP00000545521.1 | ||||
| ENSG00000285530 | ENST00000835180.1 | n.139+20768_139+20774delTTTTTTT | intron | N/A |
Frequencies
GnomAD3 genomes 0.0000322 AC: 4AN: 124174Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
124174
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000322 AC: 4AN: 124174Hom.: 0 Cov.: 31 AF XY: 0.0000502 AC XY: 3AN XY: 59802 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
124174
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
59802
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33728
American (AMR)
AF:
AC:
0
AN:
12366
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2974
East Asian (EAS)
AF:
AC:
0
AN:
4216
South Asian (SAS)
AF:
AC:
0
AN:
4020
European-Finnish (FIN)
AF:
AC:
2
AN:
6890
Middle Eastern (MID)
AF:
AC:
0
AN:
262
European-Non Finnish (NFE)
AF:
AC:
2
AN:
57224
Other (OTH)
AF:
AC:
0
AN:
1722
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.638
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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