chr19-10823843-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 3P and 16B. PM1PP2BP4_StrongBP6_Very_StrongBS1
The NM_001005361.3(DNM2):c.1837G>A(p.Val613Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,613,700 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 (★★). Synonymous variant affecting the same amino acid position (i.e. V613V) has been classified as Likely benign.
Frequency
Consequence
NM_001005361.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNM2 | NM_001005361.3 | c.1837G>A | p.Val613Met | missense_variant | 17/21 | ENST00000389253.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNM2 | ENST00000389253.9 | c.1837G>A | p.Val613Met | missense_variant | 17/21 | 5 | NM_001005361.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251014Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135798
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461618Hom.: 0 Cov.: 33 AF XY: 0.0000564 AC XY: 41AN XY: 727102
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152082Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 24, 2017 | - - |
Charcot-Marie-Tooth disease dominant intermediate B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 26, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at