chr10-21930627-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022365.4(DNAJC1):c.223-1486A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,024 control chromosomes in the GnomAD database, including 27,456 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 0.57 ( 27456 hom., cov: 31)
Consequence
DNAJC1
NM_022365.4 intron
NM_022365.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.11
Genes affected
DNAJC1 (HGNC:20090): (DnaJ heat shock protein family (Hsp40) member C1) The membrane protein encoded by this gene is a DNAJ-like heat shock protein that binds the molecular chaperone BiP. In addition, the encoded protein contains two SANT domains that have been shown to bind serpin alpha1-antichymotrypsin and inter-alpha trypsin inhibitor heavy chain 4. [provided by RefSeq, Jul 2016]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC1 | NM_022365.4 | c.223-1486A>G | intron_variant | ENST00000376980.8 | |||
DNAJC1 | XM_011519614.4 | c.223-1486A>G | intron_variant | ||||
DNAJC1 | XM_017016536.3 | c.223-1486A>G | intron_variant | ||||
DNAJC1 | XM_047425628.1 | c.223-1486A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC1 | ENST00000376980.8 | c.223-1486A>G | intron_variant | 1 | NM_022365.4 | P1 | |||
DNAJC1 | ENST00000476103.3 | c.223-1486A>G | intron_variant, NMD_transcript_variant | 2 | |||||
DNAJC1 | ENST00000376946.2 | n.558-1486A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
DNAJC1 | ENST00000447548.5 | n.188-1486A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.573 AC: 87109AN: 151906Hom.: 27452 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.573 AC: 87128AN: 152024Hom.: 27456 Cov.: 31 AF XY: 0.579 AC XY: 43041AN XY: 74302
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2695
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
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