rs3790436
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001256864.2(DNAJC6):c.2635-1082G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,958 control chromosomes in the GnomAD database, including 18,182 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.48 ( 18182 hom., cov: 32)
Consequence
DNAJC6
NM_001256864.2 intron
NM_001256864.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.77
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC6 | NM_001256864.2 | c.2635-1082G>C | intron_variant | ENST00000371069.5 | |||
DNAJC6 | NM_001256865.2 | c.2425-1082G>C | intron_variant | ||||
DNAJC6 | NM_014787.4 | c.2464-1082G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC6 | ENST00000371069.5 | c.2635-1082G>C | intron_variant | 1 | NM_001256864.2 | P4 | |||
DNAJC6 | ENST00000395325.7 | c.2464-1082G>C | intron_variant | 1 | A1 | ||||
DNAJC6 | ENST00000263441.11 | c.2425-1082G>C | intron_variant | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.484 AC: 73437AN: 151840Hom.: 18168 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.484 AC: 73474AN: 151958Hom.: 18182 Cov.: 32 AF XY: 0.484 AC XY: 35912AN XY: 74258
GnomAD4 genome
?
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73474
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151958
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32
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35912
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74258
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1994
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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