6-28297909-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032507.4(PGBD1):āc.787A>Gā(p.Thr263Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 1,518,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032507.4 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 |
---|---|---|---|---|---|---|---|
PGBD1 | NM_032507.4 | c.787A>G | p.Thr263Ala | missense_variant | 6/7 | ENST00000682144.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGBD1 | ENST00000682144.1 | c.787A>G | p.Thr263Ala | missense_variant | 6/7 | NM_032507.4 | P1 | ||
PGBD1 | ENST00000259883.3 | c.787A>G | p.Thr263Ala | missense_variant | 6/7 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000136 AC: 2AN: 147556Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247074Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133750
GnomAD4 exome AF: 0.00000584 AC: 8AN: 1370498Hom.: 0 Cov.: 30 AF XY: 0.00000293 AC XY: 2AN XY: 682746
GnomAD4 genome AF: 0.0000136 AC: 2AN: 147556Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 71604
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at