19-14518334-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_006145.3(DNAJB1):āc.16T>Cā(p.Tyr6His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,591,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006145.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJB1 | NM_006145.3 | c.16T>C | p.Tyr6His | missense_variant | 1/3 | ENST00000254322.3 | NP_006136.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJB1 | ENST00000254322.3 | c.16T>C | p.Tyr6His | missense_variant | 1/3 | 1 | NM_006145.3 | ENSP00000254322.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000446 AC: 1AN: 224030Hom.: 0 AF XY: 0.00000812 AC XY: 1AN XY: 123214
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1439360Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 716408
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.16T>C (p.Y6H) alteration is located in exon 1 (coding exon 1) of the DNAJB1 gene. This alteration results from a T to C substitution at nucleotide position 16, causing the tyrosine (Y) at amino acid position 6 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