15-40768000-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_018163.3(DNAJC17):c.855C>G(p.Ala285=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,605,638 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. A285A) has been classified as Likely benign.
Frequency
Consequence
NM_018163.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC17 | NM_018163.3 | c.855C>G | p.Ala285= | synonymous_variant | 11/11 | ENST00000220496.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC17 | ENST00000220496.9 | c.855C>G | p.Ala285= | synonymous_variant | 11/11 | 1 | NM_018163.3 | P1 | |
DNAJC17 | ENST00000558727.1 | n.420C>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
DNAJC17 | ENST00000561110.5 | n.402C>G | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
DNAJC17 | ENST00000559238.5 | c.*883C>G | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240780Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130824
GnomAD4 exome AF: 0.00000550 AC: 8AN: 1453462Hom.: 0 Cov.: 33 AF XY: 0.00000553 AC XY: 4AN XY: 723318
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
DNAJC17-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at