rs1570868
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001256864.2(DNAJC6):c.344+140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 1,207,840 control chromosomes in the GnomAD database, including 188,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 21711 hom., cov: 31)
Exomes 𝑓: 0.56 ( 166519 hom. )
Consequence
DNAJC6
NM_001256864.2 intron
NM_001256864.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.72
Genes affected
DNAJC6 (HGNC:15469): (DnaJ heat shock protein family (Hsp40) member C6) DNAJC6 belongs to the evolutionarily conserved DNAJ/HSP40 family of proteins, which regulate molecular chaperone activity by stimulating ATPase activity. DNAJ proteins may have up to 3 distinct domains: a conserved 70-amino acid J domain, usually at the N terminus, a glycine/phenylalanine (G/F)-rich region, and a cysteine-rich domain containing 4 motifs resembling a zinc finger domain (Ohtsuka and Hata, 2000 [PubMed 11147971]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 1-65364925-T-C is Benign according to our data. Variant chr1-65364925-T-C is described in ClinVar as [Benign]. Clinvar id is 1222461.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC6 | NM_001256864.2 | c.344+140T>C | intron_variant | ENST00000371069.5 | |||
DNAJC6 | NM_001256865.2 | c.134+140T>C | intron_variant | ||||
DNAJC6 | NM_014787.4 | c.173+140T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC6 | ENST00000371069.5 | c.344+140T>C | intron_variant | 1 | NM_001256864.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.531 AC: 80570AN: 151796Hom.: 21709 Cov.: 31
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GnomAD4 exome AF: 0.556 AC: 587056AN: 1055926Hom.: 166519 AF XY: 0.559 AC XY: 296221AN XY: 529750
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GnomAD4 genome ? AF: 0.531 AC: 80613AN: 151914Hom.: 21711 Cov.: 31 AF XY: 0.525 AC XY: 38942AN XY: 74198
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at