22-40861585-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145174.2(DNAJB7):c.410T>G(p.Phe137Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB7 | NM_145174.2 | c.410T>G | p.Phe137Cys | missense_variant | 1/1 | ENST00000307221.5 | |
XPNPEP3 | NM_022098.4 | c.64+4340A>C | intron_variant | ENST00000357137.9 | |||
XPNPEP3 | NM_001204827.2 | c.*13-33A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB7 | ENST00000307221.5 | c.410T>G | p.Phe137Cys | missense_variant | 1/1 | NM_145174.2 | P1 | ||
XPNPEP3 | ENST00000357137.9 | c.64+4340A>C | intron_variant | 1 | NM_022098.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461038Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726774
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.410T>G (p.F137C) 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 410, causing the phenylalanine (F) at amino acid position 137 to be replaced by a cysteine (C). 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