11-31430334-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181706.5(DNAJC24):c.383C>T(p.Ala128Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,610,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181706.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC24 | NM_181706.5 | c.383C>T | p.Ala128Val | missense_variant | 5/5 | ENST00000465995.6 | NP_859057.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC24 | ENST00000465995.6 | c.383C>T | p.Ala128Val | missense_variant | 5/5 | 1 | NM_181706.5 | ENSP00000417548.1 | ||
DNAJC24 | ENST00000395949.2 | n.*168C>T | non_coding_transcript_exon_variant | 3/3 | 3 | ENSP00000379279.2 | ||||
DNAJC24 | ENST00000530125.1 | n.364C>T | non_coding_transcript_exon_variant | 3/3 | 5 | |||||
DNAJC24 | ENST00000395949.2 | n.*168C>T | 3_prime_UTR_variant | 3/3 | 3 | ENSP00000379279.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152000Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248570Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134880
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1458910Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 725744
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152000Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.383C>T (p.A128V) alteration is located in exon 5 (coding exon 4) of the DNAJC24 gene. This alteration results from a C to T substitution at nucleotide position 383, causing the alanine (A) at amino acid position 128 to be replaced by a valine (V). 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