chr18-34812016-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001386795.1(DTNA):āc.506A>Gā(p.Gln169Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,126 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 Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. Q169Q) has been classified as Likely benign.
Frequency
Consequence
NM_001386795.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DTNA | NM_001386795.1 | c.506A>G | p.Gln169Arg | missense_variant | 6/23 | ENST00000444659.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DTNA | ENST00000444659.6 | c.506A>G | p.Gln169Arg | missense_variant | 6/23 | 5 | NM_001386795.1 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251216Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135764
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727196
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74484
ClinVar
Submissions by phenotype
Left ventricular noncompaction 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 30, 2019 | This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamine with arginine at codon 169 of the DTNA protein (p.Gln169Arg). The glutamine residue is moderately conserved and there is a small physicochemical difference between glutamine and arginine. This variant has not been reported in the literature in individuals with DTNA-related disease. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at