22-40861749-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145174.2(DNAJB7):c.246T>G(p.Asp82Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145174.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB7 | NM_145174.2 | c.246T>G | p.Asp82Glu | missense_variant | 1/1 | ENST00000307221.5 | |
XPNPEP3 | NM_022098.4 | c.64+4504A>C | intron_variant | ENST00000357137.9 | |||
XPNPEP3 | NM_001204827.2 | c.*144A>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB7 | ENST00000307221.5 | c.246T>G | p.Asp82Glu | missense_variant | 1/1 | NM_145174.2 | P1 | ||
XPNPEP3 | ENST00000357137.9 | c.64+4504A>C | intron_variant | 1 | NM_022098.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250440Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135322
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461200Hom.: 0 Cov.: 31 AF XY: 0.0000991 AC XY: 72AN XY: 726874
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.246T>G (p.D82E) alteration is located in exon 1 (coding exon 1) of the DNAJB7 gene. This alteration results from a T to G substitution at nucleotide position 246, causing the aspartic acid (D) at amino acid position 82 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at