6-32187284-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002586.5(PBX2):c.982G>T(p.Gly328Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,612,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002586.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PBX2 | NM_002586.5 | c.982G>T | p.Gly328Cys | missense_variant | 6/9 | ENST00000375050.6 | NP_002577.2 | |
PBX2 | XM_047418839.1 | c.637G>T | p.Gly213Cys | missense_variant | 5/8 | XP_047274795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PBX2 | ENST00000375050.6 | c.982G>T | p.Gly328Cys | missense_variant | 6/9 | 1 | NM_002586.5 | ENSP00000364190.3 | ||
PBX2 | ENST00000478678.5 | n.1009G>T | non_coding_transcript_exon_variant | 6/6 | 1 | |||||
PBX2 | ENST00000495300.1 | n.232G>T | non_coding_transcript_exon_variant | 1/2 | 3 | |||||
PBX2 | ENST00000496171.1 | n.999G>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000126 AC: 31AN: 246532Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134404
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460746Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726694
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.982G>T (p.G328C) alteration is located in exon 6 (coding exon 6) of the PBX2 gene. This alteration results from a G to T substitution at nucleotide position 982, causing the glycine (G) at amino acid position 328 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