X-18757640-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001377996.1(PPEF1):āc.410A>Gā(p.His137Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,203,453 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001377996.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPEF1 | NM_001377996.1 | c.410A>G | p.His137Arg | missense_variant | 5/16 | ENST00000470157.2 | NP_001364925.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPEF1 | ENST00000470157.2 | c.410A>G | p.His137Arg | missense_variant | 5/16 | 3 | NM_001377996.1 | ENSP00000419273.2 |
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 111794Hom.: 0 Cov.: 22 AF XY: 0.0000588 AC XY: 2AN XY: 33992
GnomAD3 exomes AF: 0.0000385 AC: 7AN: 181594Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66144
GnomAD4 exome AF: 0.0000311 AC: 34AN: 1091659Hom.: 0 Cov.: 27 AF XY: 0.0000252 AC XY: 9AN XY: 357381
GnomAD4 genome AF: 0.0000268 AC: 3AN: 111794Hom.: 0 Cov.: 22 AF XY: 0.0000588 AC XY: 2AN XY: 33992
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 09, 2024 | The c.410A>G (p.H137R) alteration is located in exon 8 (coding exon 5) of the PPEF1 gene. This alteration results from a A to G substitution at nucleotide position 410, causing the histidine (H) at amino acid position 137 to be replaced by an arginine (R). 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