NM_001317100.2:c.73C>T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PVS1_StrongBP6BS1BS2
The NM_001317100.2(DNAJB4):c.73C>T(p.Arg25*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 152,066 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001317100.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJB4 | NM_001317100.2 | c.73C>T | p.Arg25* | stop_gained | Exon 2 of 4 | NP_001304029.1 | ||
DNAJB4 | NM_001317099.2 | c.-31-12232C>T | intron_variant | Intron 1 of 3 | NP_001304028.1 | |||
DNAJB4 | NM_001317101.2 | c.-135+13229C>T | intron_variant | Intron 1 of 2 | NP_001304030.1 | |||
DNAJB4 | NM_001317102.2 | c.-135+13555C>T | intron_variant | Intron 1 of 2 | NP_001304031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJB4 | ENST00000426517.1 | c.-31-12232C>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000399494.1 | ||||
DNAJB4 | ENST00000477671.2 | n.255C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 | |||||
GIPC2 | ENST00000476882.1 | n.78+13229C>T | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1544AN: 151948Hom.: 33 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 104Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 78
GnomAD4 genome AF: 0.0101 AC: 1543AN: 152066Hom.: 33 Cov.: 32 AF XY: 0.00972 AC XY: 723AN XY: 74352
ClinVar
Submissions by phenotype
DNAJB4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at