12-45036046-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001004329.3(DBX2):c.472C>T(p.Arg158Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000359 in 1,613,496 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R158H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001004329.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DBX2 | NM_001004329.3 | c.472C>T | p.Arg158Cys | missense_variant | 2/4 | ENST00000332700.6 | |
LOC105369742 | XR_944885.3 | n.203+801G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBX2 | ENST00000332700.6 | c.472C>T | p.Arg158Cys | missense_variant | 2/4 | 2 | NM_001004329.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247202Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134022
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461208Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 726860
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.472C>T (p.R158C) alteration is located in exon 2 (coding exon 2) of the DBX2 gene. This alteration results from a C to T substitution at nucleotide position 472, causing the arginine (R) at amino acid position 158 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