17-41990222-TG-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003315.4(DNAJC7):c.599+41delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 1,546,384 control chromosomes in the GnomAD database, including 5,452 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.11 ( 1113 hom., cov: 30)
Exomes 𝑓: 0.072 ( 4339 hom. )
Consequence
DNAJC7
NM_003315.4 intron
NM_003315.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.17
Genes affected
DNAJC7 (HGNC:12392): (DnaJ heat shock protein family (Hsp40) member C7) This gene encodes a member of the DNAJ heat shock protein 40 family of proteins that is characterized by two N-terminal tetratricopeptide repeat domains and a C-terminal DNAJ domain. This protein binds the chaperone proteins heat shock proteins 70 and 90 in an ATP-dependent manner and may function as a co-chaperone. Pseudogenes of this gene are found on chromosomes 1 and 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 17-41990222-TG-T is Benign according to our data. Variant chr17-41990222-TG-T is described in ClinVar as [Benign]. Clinvar id is 1245936.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC7 | NM_003315.4 | c.599+41delC | intron_variant | ENST00000457167.9 | NP_003306.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC7 | ENST00000457167.9 | c.599+41delC | intron_variant | 1 | NM_003315.4 | ENSP00000406463.2 |
Frequencies
GnomAD3 genomes AF: 0.107 AC: 16292AN: 152106Hom.: 1099 Cov.: 30
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GnomAD3 exomes AF: 0.0839 AC: 15313AN: 182436Hom.: 804 AF XY: 0.0854 AC XY: 8283AN XY: 96948
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GnomAD4 exome AF: 0.0721 AC: 100580AN: 1394160Hom.: 4339 Cov.: 23 AF XY: 0.0731 AC XY: 50459AN XY: 690232
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GnomAD4 genome AF: 0.107 AC: 16353AN: 152224Hom.: 1113 Cov.: 30 AF XY: 0.108 AC XY: 8038AN XY: 74426
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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 | May 11, 2021 | - - |
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