chr1-65364610-G-GT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001256864.2(DNAJC6):c.194-22dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00214 in 1,441,052 control chromosomes in the GnomAD database, including 55 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00091 ( 3 hom., cov: 31)
Exomes 𝑓: 0.0023 ( 52 hom. )
Consequence
DNAJC6
NM_001256864.2 intron
NM_001256864.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.645
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 -10 ACMG points.
BP6
?
Variant 1-65364610-G-GT is Benign according to our data. Variant chr1-65364610-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 1197078.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00226 (2970/1314184) while in subpopulation EAS AF= 0.0413 (1388/33600). AF 95% confidence interval is 0.0395. There are 52 homozygotes in gnomad4_exome. There are 1521 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC6 | NM_001256864.2 | c.194-22dup | intron_variant | ENST00000371069.5 | |||
DNAJC6 | NM_001256865.2 | c.-17-22dup | intron_variant | ||||
DNAJC6 | NM_014787.4 | c.23-22dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC6 | ENST00000371069.5 | c.194-22dup | intron_variant | 1 | NM_001256864.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000907 AC: 115AN: 126848Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.0103 AC: 1019AN: 99252Hom.: 58 AF XY: 0.00994 AC XY: 520AN XY: 52302
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GnomAD4 exome AF: 0.00226 AC: 2970AN: 1314184Hom.: 52 Cov.: 30 AF XY: 0.00233 AC XY: 1521AN XY: 653042
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GnomAD4 genome ? AF: 0.000906 AC: 115AN: 126868Hom.: 3 Cov.: 31 AF XY: 0.00101 AC XY: 62AN XY: 61216
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 20, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at