1-6640071-CAAAAAA-CAAAAAAA
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000377577.10(DNAJC11):c.1098-15_1098-14insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.47 ( 6434 hom., cov: 0)
Exomes 𝑓: 0.20 ( 300 hom. )
Consequence
DNAJC11
ENST00000377577.10 splice_polypyrimidine_tract, intron
ENST00000377577.10 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
DNAJC11 (HGNC:25570): (DnaJ heat shock protein family (Hsp40) member C11) Involved in cristae formation. Located in mitochondrial outer membrane and nuclear speck. Part of MIB complex. Colocalizes with MICOS complex and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-6640071-C-CA is Benign according to our data. Variant chr1-6640071-C-CA is described in ClinVar as [Benign]. Clinvar id is 402790.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC11 | NM_018198.4 | c.1098-15_1098-14insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000377577.10 | NP_060668.2 | |||
DNAJC11 | XM_047424842.1 | c.828-15_828-14insT | splice_polypyrimidine_tract_variant, intron_variant | XP_047280798.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC11 | ENST00000377577.10 | c.1098-15_1098-14insT | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018198.4 | ENSP00000366800 | P1 |
Frequencies
GnomAD3 genomes AF: 0.466 AC: 38439AN: 82518Hom.: 6442 Cov.: 0
GnomAD3 genomes
AF:
AC:
38439
AN:
82518
Hom.:
Cov.:
0
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: 0.173 AC: 4575AN: 26422Hom.: 52 AF XY: 0.176 AC XY: 2340AN XY: 13270
GnomAD3 exomes
AF:
AC:
4575
AN:
26422
Hom.:
AF XY:
AC XY:
2340
AN XY:
13270
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: 0.204 AC: 225843AN: 1106338Hom.: 300 Cov.: 0 AF XY: 0.204 AC XY: 108782AN XY: 533998
GnomAD4 exome
AF:
AC:
225843
AN:
1106338
Hom.:
Cov.:
0
AF XY:
AC XY:
108782
AN XY:
533998
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: 0.466 AC: 38409AN: 82490Hom.: 6434 Cov.: 0 AF XY: 0.465 AC XY: 17866AN XY: 38396
GnomAD4 genome
AF:
AC:
38409
AN:
82490
Hom.:
Cov.:
0
AF XY:
AC XY:
17866
AN XY:
38396
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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