20-63895274-A-AGCGGAGCC
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_025219.3(DNAJC5):c.-51_-44dupCGGAGCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00976 in 146,394 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_025219.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC5 | ENST00000360864 | c.-51_-44dupCGGAGCCG | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_025219.3 | ENSP00000354111.4 | |||
DNAJC5 | ENST00000470551.1 | n.-51_-44dupCGGAGCCG | non_coding_transcript_exon_variant | Exon 1 of 6 | 2 | ENSP00000434744.1 | ||||
DNAJC5 | ENST00000470551.1 | n.-51_-44dupCGGAGCCG | 5_prime_UTR_variant | Exon 1 of 6 | 2 | ENSP00000434744.1 | ||||
ENSG00000290226 | ENST00000703636.1 | n.453+12464_453+12471dupCGGAGCCG | intron_variant | Intron 4 of 4 |
Frequencies
GnomAD3 genomes AF: 0.00977 AC: 1430AN: 146302Hom.: 8 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 870Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 424
GnomAD4 genome AF: 0.00976 AC: 1429AN: 146394Hom.: 8 Cov.: 32 AF XY: 0.00930 AC XY: 663AN XY: 71310
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at