NM_001005361.3:c.2592C>T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_001005361.3(DNM2):c.2592C>T(p.Ala864Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,610,918 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A864A) has been classified as Likely benign.
Frequency
Consequence
NM_001005361.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant centronuclear myopathyInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- Charcot-Marie-Tooth diseaseInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- Charcot-Marie-Tooth disease dominant intermediate BInheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
- autosomal dominant Charcot-Marie-Tooth disease type 2MInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- fetal akinesia-cerebral and retinal hemorrhage syndromeInheritance: AR Classification: SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
- hereditary spastic paraplegiaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152062Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000183 AC: 44AN: 239984 AF XY: 0.000199 show subpopulations
GnomAD4 exome AF: 0.000191 AC: 278AN: 1458738Hom.: 0 Cov.: 31 AF XY: 0.000203 AC XY: 147AN XY: 725420 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000138 AC: 21AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74388 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Charcot-Marie-Tooth disease dominant intermediate B Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at