rs570093404
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001386795.1(DTNA):c.1770C>A(p.Ser590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,128 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. S590S) has been classified as Likely benign.
Frequency
Consequence
NM_001386795.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTNA | NM_001386795.1 | c.1770C>A | p.Ser590= | synonymous_variant | 18/23 | ENST00000444659.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTNA | ENST00000444659.6 | c.1770C>A | p.Ser590= | synonymous_variant | 18/23 | 5 | NM_001386795.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251174Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135800
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727168
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 12, 2013 | Ser506Ser in exon 17 of DTNA: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. Ser506Ser in exon 17 of DTNA (allele frequenc y = n/a) - |
Left ventricular noncompaction 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 11, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at