1-15536478-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015291.4(DNAJC16):c.238C>T(p.Leu80Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000318 in 1,572,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015291.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC16 | NM_015291.4 | c.238C>T | p.Leu80Phe | missense_variant | Exon 4 of 15 | ENST00000375847.8 | NP_056106.1 | |
DNAJC16 | NM_001287811.2 | c.-699C>T | 5_prime_UTR_variant | Exon 3 of 14 | NP_001274740.1 | |||
DNAJC16 | NR_109898.2 | n.367C>T | non_coding_transcript_exon_variant | Exon 4 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000282 AC: 4AN: 1420486Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 703760
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152062Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.238C>T (p.L80F) alteration is located in exon 4 (coding exon 3) of the DNAJC16 gene. This alteration results from a C to T substitution at nucleotide position 238, causing the leucine (L) at amino acid position 80 to be replaced by a phenylalanine (F). 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