18-34679573-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001198938.2(DTNA):c.-21G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000191 in 152,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
DTNA
NM_001198938.2 5_prime_UTR
NM_001198938.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.11
Publications
0 publications found
Genes affected
DTNA (HGNC:3057): (dystrobrevin alpha) The protein encoded by this gene belongs to the dystrobrevin subfamily of the dystrophin family. This protein is a component of the dystrophin-associated protein complex (DPC), which consists of dystrophin and several integral and peripheral membrane proteins, including dystroglycans, sarcoglycans, syntrophins and alpha- and beta-dystrobrevin. The DPC localizes to the sarcolemma and its disruption is associated with various forms of muscular dystrophy. Mutations in this gene are associated with left ventricular noncompaction with congenital heart defects. Multiple alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
DTNA Gene-Disease associations (from GenCC):
- left ventricular noncompaction 1Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- Meniere diseaseInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- congenital heart diseaseInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
- dilated cardiomyopathyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
Variant 18-34679573-G-A is Benign according to our data. Variant chr18-34679573-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 377814.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 29 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001198938.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DTNA | NM_001198938.2 | c.-21G>A | 5_prime_UTR | Exon 2 of 20 | NP_001185867.1 | Q9Y4J8-15 | |||
| DTNA | NM_001386754.1 | c.-21G>A | 5_prime_UTR | Exon 2 of 22 | NP_001373683.1 | A0A7P0Z4D7 | |||
| DTNA | NM_001386755.1 | c.-21G>A | 5_prime_UTR | Exon 2 of 22 | NP_001373684.1 | A0A7P0Z4D7 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DTNA | ENST00000598334.5 | TSL:1 | c.-21G>A | 5_prime_UTR | Exon 2 of 20 | ENSP00000470152.1 | Q9Y4J8-15 | ||
| DTNA | ENST00000399121.9 | TSL:1 | c.-21G>A | 5_prime_UTR | Exon 2 of 22 | ENSP00000382072.5 | Q9Y4J8-14 | ||
| DTNA | ENST00000598142.5 | TSL:1 | c.-21G>A | 5_prime_UTR | Exon 1 of 21 | ENSP00000470716.1 | Q9Y4J8-2 |
Frequencies
GnomAD3 genomes 0.000191 AC: 29AN: 152182Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
29
AN:
152182
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome 0.000191 AC: 29AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74342 show subpopulations
GnomAD4 genome
AF:
AC:
29
AN:
152182
Hom.:
Cov.:
32
AF XY:
AC XY:
10
AN XY:
74342
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41452
American (AMR)
AF:
AC:
0
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
22
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
AC:
0
AN:
10614
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
5
AN:
68036
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
2
4
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11
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0.60
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0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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10
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Age
Alfa
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ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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