chr22-40861075-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145174.2(DNAJB7):c.920G>A(p.Arg307Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,434,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJB7 | NM_145174.2 | c.920G>A | p.Arg307Lys | missense_variant | 1/1 | ENST00000307221.5 | NP_660157.1 | |
XPNPEP3 | NM_022098.4 | c.64+3830C>T | intron_variant | ENST00000357137.9 | NP_071381.1 | |||
XPNPEP3 | NM_001204827.2 | c.*12+282C>T | intron_variant | NP_001191756.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJB7 | ENST00000307221.5 | c.920G>A | p.Arg307Lys | missense_variant | 1/1 | NM_145174.2 | ENSP00000307197 | P1 | ||
XPNPEP3 | ENST00000357137.9 | c.64+3830C>T | intron_variant | 1 | NM_022098.4 | ENSP00000349658 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000438 AC: 1AN: 228448Hom.: 0 AF XY: 0.00000810 AC XY: 1AN XY: 123458
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1434058Hom.: 0 Cov.: 31 AF XY: 0.00000281 AC XY: 2AN XY: 711796
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.920G>A (p.R307K) alteration is located in exon 1 (coding exon 1) of the DNAJB7 gene. This alteration results from a G to A substitution at nucleotide position 920, causing the arginine (R) at amino acid position 307 to be replaced by a lysine (K). 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