chr6-32162807-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005155.7(PPT2):c.766G>A(p.Val256Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,260 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005155.7 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPT2 | NM_005155.7 | c.766G>A | p.Val256Ile | missense_variant, splice_region_variant | 9/9 | ENST00000324816.11 | |
PPT2-EGFL8 | NR_037861.1 | n.1179+185G>A | intron_variant, non_coding_transcript_variant | ||||
PPT2 | NM_138717.3 | c.784G>A | p.Val262Ile | missense_variant, splice_region_variant | 9/9 | ||
PPT2 | NM_001204103.2 | c.766G>A | p.Val256Ile | missense_variant, splice_region_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPT2 | ENST00000324816.11 | c.766G>A | p.Val256Ile | missense_variant, splice_region_variant | 9/9 | 1 | NM_005155.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250002Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135146
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1460966Hom.: 1 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726814
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | May 12, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at