rs144763522
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM1PP2BP4_ModerateBP6
The NM_001005361.3(DNM2):c.1645T>A(p.Ser549Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,609,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001005361.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNM2 | NM_001005361.3 | c.1645T>A | p.Ser549Thr | missense_variant | 15/21 | ENST00000389253.9 | NP_001005361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNM2 | ENST00000389253.9 | c.1645T>A | p.Ser549Thr | missense_variant | 15/21 | 5 | NM_001005361.3 | ENSP00000373905 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 244154Hom.: 0 AF XY: 0.0000378 AC XY: 5AN XY: 132348
GnomAD4 exome AF: 0.00000892 AC: 13AN: 1457658Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 724906
GnomAD4 genome AF: 0.000118 AC: 18AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74260
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 08, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 28, 2019 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | 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
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at