chr5-34929869-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001012339.3(DNAJC21):āc.50A>Gā(p.Glu17Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00016 in 1,573,004 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001012339.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC21 | NM_001012339.3 | c.50A>G | p.Glu17Gly | missense_variant | Exon 1 of 12 | ENST00000648817.1 | NP_001012339.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000860 AC: 13AN: 151146Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000191 AC: 42AN: 219976Hom.: 0 AF XY: 0.000133 AC XY: 16AN XY: 120714
GnomAD4 exome AF: 0.000167 AC: 238AN: 1421740Hom.: 4 Cov.: 31 AF XY: 0.000160 AC XY: 113AN XY: 707522
GnomAD4 genome AF: 0.0000859 AC: 13AN: 151264Hom.: 0 Cov.: 29 AF XY: 0.0000947 AC XY: 7AN XY: 73920
ClinVar
Submissions by phenotype
not specified Uncertain:1
DNA sequence analysis of the DNAJC21 gene demonstrated a sequence change, c.50A>G, in exon 1 that results in an amino acid change, p.Glu17Gly. This sequence change does not appear to have been previously described in individuals with DNAJC21-related disorders. This sequence change has been described in the gnomAD database with a frequency of of 0.26% in the East Asian subpopulation and an overall frequency of 0.018% (dbSNP rs761693334). The p.Glu17Gly change affects a moderately conserved amino acid residue located in a domain of the DNAJC21 protein that is known to be functional. The p.Glu17Gly substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Glu17Gly change remains unknown at this time. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at