chr1-58536610-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145243.5(OMA1):āc.632T>Gā(p.Phe211Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0225 in 872,832 control chromosomes in the GnomAD database, including 565 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.018 ( 57 hom., cov: 32)
Exomes š: 0.023 ( 508 hom. )
Consequence
OMA1
NM_145243.5 missense
NM_145243.5 missense
Scores
1
8
9
Clinical Significance
Conservation
PhyloP100: 5.64
Genes affected
OMA1 (HGNC:29661): (OMA1 zinc metallopeptidase) Enables metalloendopeptidase activity. Involved in several processes, including HRI-mediated signaling; proteolysis; and regulation of mitochondrion organization. Located in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Apr 2022]
DAB1 (HGNC:2661): (DAB adaptor protein 1) The laminar organization of multiple neuronal types in the cerebral cortex is required for normal cognitive function. In mice, the disabled-1 gene plays a central role in brain development, directing the migration of cortical neurons past previously formed neurons to reach their proper layer. This gene is similar to disabled-1, and the protein encoded by this gene is thought to be a signal transducer that interacts with protein kinase pathways to regulate neuronal positioning in the developing brain. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.002847284).
BP6
Variant 1-58536610-A-C is Benign according to our data. Variant chr1-58536610-A-C is described in ClinVar as [Benign]. Clinvar id is 1287065.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OMA1 | NM_145243.5 | c.632T>G | p.Phe211Cys | missense_variant | 3/9 | ENST00000371226.8 | |
DAB1 | NM_001379461.1 | c.-729-9275T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OMA1 | ENST00000371226.8 | c.632T>G | p.Phe211Cys | missense_variant | 3/9 | 1 | NM_145243.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0185 AC: 2816AN: 152172Hom.: 57 Cov.: 32
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GnomAD3 exomes AF: 0.0265 AC: 6665AN: 251320Hom.: 228 AF XY: 0.0279 AC XY: 3794AN XY: 135832
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GnomAD4 exome AF: 0.0234 AC: 16829AN: 720542Hom.: 508 Cov.: 0 AF XY: 0.0248 AC XY: 9556AN XY: 384630
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GnomAD4 genome AF: 0.0185 AC: 2813AN: 152290Hom.: 57 Cov.: 32 AF XY: 0.0198 AC XY: 1478AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 32236861) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.;.
MutationTaster
Benign
P;P
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;.;.;.
Polyphen
D;.;.;.
Vest4
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at