chr12-32679332-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001278464.2(DNM1L):c.-32G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,484,520 control chromosomes in the GnomAD database, including 538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.036 ( 265 hom., cov: 33)
Exomes 𝑓: 0.011 ( 273 hom. )
Consequence
DNM1L
NM_001278464.2 5_prime_UTR
NM_001278464.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.581
Genes affected
DNM1L (HGNC:2973): (dynamin 1 like) This gene encodes a member of the dynamin superfamily of GTPases. The encoded protein mediates mitochondrial and peroxisomal division, and is involved in developmentally regulated apoptosis and programmed necrosis. Dysfunction of this gene is implicated in several neurological disorders, including Alzheimer's disease. Mutations in this gene are associated with the autosomal dominant disorder, encephalopathy, lethal, due to defective mitochondrial and peroxisomal fission (EMPF). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 12-32679332-G-T is Benign according to our data. Variant chr12-32679332-G-T is described in ClinVar as [Benign]. Clinvar id is 137129.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNM1L | NM_001278464.2 | c.-32G>T | 5_prime_UTR_variant | 1/21 | ENST00000553257.6 | ||
DNM1L | NM_012062.5 | c.-32G>T | 5_prime_UTR_variant | 1/20 | ENST00000549701.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNM1L | ENST00000549701.6 | c.-32G>T | 5_prime_UTR_variant | 1/20 | 1 | NM_012062.5 | |||
DNM1L | ENST00000553257.6 | c.-32G>T | 5_prime_UTR_variant | 1/21 | 2 | NM_001278464.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0359 AC: 5459AN: 152242Hom.: 263 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
5459
AN:
152242
Hom.:
Cov.:
33
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:
GnomAD3 exomes AF: 0.0132 AC: 3126AN: 236356Hom.: 104 AF XY: 0.0113 AC XY: 1455AN XY: 128482
GnomAD3 exomes
AF:
AC:
3126
AN:
236356
Hom.:
AF XY:
AC XY:
1455
AN XY:
128482
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0109 AC: 14519AN: 1332160Hom.: 273 Cov.: 19 AF XY: 0.0105 AC XY: 7019AN XY: 669320
GnomAD4 exome
AF:
AC:
14519
AN:
1332160
Hom.:
Cov.:
19
AF XY:
AC XY:
7019
AN XY:
669320
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0359 AC: 5475AN: 152360Hom.: 265 Cov.: 33 AF XY: 0.0348 AC XY: 2591AN XY: 74516
GnomAD4 genome
?
AF:
AC:
5475
AN:
152360
Hom.:
Cov.:
33
AF XY:
AC XY:
2591
AN XY:
74516
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
23
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 26, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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