chr9-128222476-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_004408.4(DNM1):c.1008C>T(p.Phe336Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 1,613,764 control chromosomes in the GnomAD database, including 236,688 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004408.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNM1 | ENST00000372923.8 | c.1008C>T | p.Phe336Phe | synonymous_variant | Exon 8 of 22 | 1 | NM_004408.4 | ENSP00000362014.4 | ||
DNM1 | ENST00000634267.2 | c.1008C>T | p.Phe336Phe | synonymous_variant | Exon 8 of 22 | 5 | ENSP00000489096.1 |
Frequencies
GnomAD3 genomes AF: 0.433 AC: 65773AN: 151902Hom.: 17215 Cov.: 32
GnomAD3 exomes AF: 0.542 AC: 136150AN: 251218Hom.: 39293 AF XY: 0.546 AC XY: 74113AN XY: 135808
GnomAD4 exome AF: 0.542 AC: 792635AN: 1461744Hom.: 219465 Cov.: 62 AF XY: 0.543 AC XY: 394906AN XY: 727172
GnomAD4 genome AF: 0.433 AC: 65779AN: 152020Hom.: 17223 Cov.: 32 AF XY: 0.439 AC XY: 32590AN XY: 74278
ClinVar
Submissions by phenotype
not specified Benign:2
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. -
This variant is classified as Benign based on local population frequency. This variant was detected in 88% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 82. Only high quality variants are reported. -
Developmental and epileptic encephalopathy, 31A Benign:2
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not provided Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at