chr21-33489128-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001040192.3(DNAJC28):c.266C>T(p.Ser89Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S89C) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Consequence
DNAJC28
NM_001040192.3 missense
NM_001040192.3 missense
Scores
11
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.16
Publications
1 publications found
Genes affected
DNAJC28 (HGNC:1297): (DnaJ heat shock protein family (Hsp40) member C28) This gene encodes a member of the DnaJ heat shock protein family. The encoded protein, which contains a conserved N-terminal DnaJ domain, is thought to play a role in protein folding or act as a molecular chaperone protein. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC28 | NM_001040192.3 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | ENST00000381947.4 | NP_001035282.1 | |
DNAJC28 | NM_001320746.3 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | NP_001307675.1 | ||
DNAJC28 | NM_017833.5 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | NP_060303.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC28 | ENST00000381947.4 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | 1 | NM_001040192.3 | ENSP00000371373.3 | ||
DNAJC28 | ENST00000314399.3 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | 1 | ENSP00000320303.3 | |||
DNAJC28 | ENST00000402202.1 | c.266C>T | p.Ser89Phe | missense_variant | Exon 2 of 2 | 5 | ENSP00000385777.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M;M;M
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
.;D;D;D
REVEL
Uncertain
Sift
Uncertain
.;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
D;D;D;D
Vest4
MutPred
Loss of disorder (P = 0.0311);Loss of disorder (P = 0.0311);Loss of disorder (P = 0.0311);Loss of disorder (P = 0.0311);
MVP
MPC
0.23
ClinPred
D
GERP RS
Varity_R
gMVP
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
Publications
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