chr3-128462789-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153330.6(DNAJB8):c.457A>C(p.Met153Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00375 in 1,613,828 control chromosomes in the GnomAD database, including 202 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_153330.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB8 | NM_153330.6 | c.457A>C | p.Met153Leu | missense_variant | 3/3 | ENST00000319153.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB8 | ENST00000319153.4 | c.457A>C | p.Met153Leu | missense_variant | 3/3 | 1 | NM_153330.6 | P1 | |
DNAJB8 | ENST00000469083.1 | c.457A>C | p.Met153Leu | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0196 AC: 2984AN: 151872Hom.: 105 Cov.: 33
GnomAD3 exomes AF: 0.00508 AC: 1276AN: 251140Hom.: 45 AF XY: 0.00353 AC XY: 480AN XY: 135822
GnomAD4 exome AF: 0.00210 AC: 3067AN: 1461838Hom.: 97 Cov.: 34 AF XY: 0.00174 AC XY: 1268AN XY: 727210
GnomAD4 genome ? AF: 0.0197 AC: 2990AN: 151990Hom.: 105 Cov.: 33 AF XY: 0.0192 AC XY: 1425AN XY: 74322
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at