rs5758111
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145174.2(DNAJB7):c.*389T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,218,696 control chromosomes in the GnomAD database, including 46 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 0.0026 ( 17 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 29 hom. )
Consequence
DNAJB7
NM_145174.2 3_prime_UTR
NM_145174.2 3_prime_UTR
Scores
5
Splicing: ADA: 0.00001992
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0960
Genes affected
DNAJB7 (HGNC:24986): (DnaJ heat shock protein family (Hsp40) member B7) The protein encoded by this intronless gene 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.[provided by RefSeq, Mar 2011]
XPNPEP3 (HGNC:28052): (X-prolyl aminopeptidase 3) The protein encoded by this gene belongs to the family of X-pro-aminopeptidases that utilize a metal cofactor, and remove the N-terminal amino acid from peptides with a proline residue in the penultimate position. This protein has been shown to localize to the mitochondria of renal cells, and have a role in ciliary function. Mutations in this gene are associated with nephronophthisis-like nephropathy-1. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene, however, expression of some of these isoforms in vivo is not known.[provided by RefSeq, Mar 2011]
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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_addAF=-0.851811).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB7 | NM_145174.2 | c.*389T>C | 3_prime_UTR_variant | 1/1 | ENST00000307221.5 | ||
XPNPEP3 | NM_022098.4 | c.64+3431A>G | intron_variant | ENST00000357137.9 | |||
XPNPEP3 | NM_001204827.2 | c.65-2A>G | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB7 | ENST00000307221.5 | c.*389T>C | 3_prime_UTR_variant | 1/1 | NM_145174.2 | P1 | |||
XPNPEP3 | ENST00000357137.9 | c.64+3431A>G | intron_variant | 1 | NM_022098.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 390AN: 151348Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00352 AC: 329AN: 93542Hom.: 4 AF XY: 0.00318 AC XY: 166AN XY: 52148
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GnomAD4 exome AF: 0.00136 AC: 1456AN: 1067230Hom.: 29 Cov.: 16 AF XY: 0.00133 AC XY: 714AN XY: 535728
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GnomAD4 genome AF: 0.00257 AC: 389AN: 151466Hom.: 17 Cov.: 32 AF XY: 0.00278 AC XY: 206AN XY: 74010
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
N;N;N;N
GERP RS
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at