5-139414161-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152686.4(DNAJC18):c.1064G>A(p.Arg355His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R355C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152686.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC18 | ENST00000302060.10 | c.1064G>A | p.Arg355His | missense_variant | Exon 8 of 8 | 1 | NM_152686.4 | ENSP00000302843.5 | ||
DNAJC18 | ENST00000510770.1 | n.370G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
DNAJC18 | ENST00000515559.2 | n.77G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | ENSP00000485339.1 | ||||
DNAJC18 | ENST00000508445.5 | c.*144G>A | downstream_gene_variant | 3 | ENSP00000426338.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251236Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135806
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727186
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1064G>A (p.R355H) alteration is located in exon 8 (coding exon 8) of the DNAJC18 gene. This alteration results from a G to A substitution at nucleotide position 1064, causing the arginine (R) at amino acid position 355 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at