chr3-128463228-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_153330.6(DNAJB8):c.18A>G(p.Glu6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00263 in 1,612,514 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 42 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 43 hom. )
Consequence
DNAJB8
NM_153330.6 synonymous
NM_153330.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
Genes affected
DNAJB8 (HGNC:23699): (DnaJ heat shock protein family (Hsp40) member B8) The protein encoded by this gene belongs to the DNAJ/HSP40 family of proteins that regulate chaperone activity. This family member suppresses aggregation and toxicity of polyglutamine proteins, and the C-terminal tail is essential for this activity. It has been implicated as a cancer-testis antigen and as a cancer stem-like cell antigen involved in renal cell carcinoma. [provided by RefSeq, Jun 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 3-128463228-T-C is Benign according to our data. Variant chr3-128463228-T-C is described in ClinVar as [Benign]. Clinvar id is 789713.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.35 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0141 (2141/152176) while in subpopulation AFR AF= 0.0472 (1961/41538). AF 95% confidence interval is 0.0455. There are 42 homozygotes in gnomad4. There are 1062 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 42 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB8 | NM_153330.6 | c.18A>G | p.Glu6= | synonymous_variant | 3/3 | ENST00000319153.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB8 | ENST00000319153.4 | c.18A>G | p.Glu6= | synonymous_variant | 3/3 | 1 | NM_153330.6 | P1 | |
DNAJB8 | ENST00000469083.1 | c.18A>G | p.Glu6= | synonymous_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0141 AC: 2139AN: 152058Hom.: 42 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2139
AN:
152058
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00373 AC: 934AN: 250222Hom.: 25 AF XY: 0.00289 AC XY: 391AN XY: 135284
GnomAD3 exomes
AF:
AC:
934
AN:
250222
Hom.:
AF XY:
AC XY:
391
AN XY:
135284
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00144 AC: 2104AN: 1460338Hom.: 43 Cov.: 38 AF XY: 0.00127 AC XY: 922AN XY: 726260
GnomAD4 exome
AF:
AC:
2104
AN:
1460338
Hom.:
Cov.:
38
AF XY:
AC XY:
922
AN XY:
726260
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0141 AC: 2141AN: 152176Hom.: 42 Cov.: 32 AF XY: 0.0143 AC XY: 1062AN XY: 74400
GnomAD4 genome
?
AF:
AC:
2141
AN:
152176
Hom.:
Cov.:
32
AF XY:
AC XY:
1062
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
14
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 | Invitae | Jun 18, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at