12-122986283-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_020845.3(PITPNM2):c.3794G>A(p.Arg1265His) variant causes a missense change. The variant allele was found at a frequency of 0.0000752 in 1,582,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R1265C) has been classified as Uncertain significance.
Frequency
Consequence
NM_020845.3 missense
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 |
---|---|---|---|---|---|---|---|
PITPNM2 | NM_020845.3 | c.3794G>A | p.Arg1265His | missense_variant | 26/26 | ENST00000320201.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITPNM2 | ENST00000320201.10 | c.3794G>A | p.Arg1265His | missense_variant | 26/26 | 5 | NM_020845.3 | P3 | |
PITPNM2 | ENST00000280562.9 | c.3776G>A | p.Arg1259His | missense_variant | 25/25 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152216Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000365 AC: 7AN: 191666Hom.: 0 AF XY: 0.0000378 AC XY: 4AN XY: 105846
GnomAD4 exome AF: 0.0000776 AC: 111AN: 1429830Hom.: 0 Cov.: 31 AF XY: 0.0000832 AC XY: 59AN XY: 709180
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152334Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.3794G>A (p.R1265H) alteration is located in exon 25 (coding exon 24) of the PITPNM2 gene. This alteration results from a G to A substitution at nucleotide position 3794, causing the arginine (R) at amino acid position 1265 to be replaced by a histidine (H). 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