NM_001286581.2:c.35G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286581.2(PHRF1):c.35G>A(p.Arg12Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,613,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R12P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001286581.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHRF1 | NM_001286581.2 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 18 | ENST00000264555.10 | NP_001273510.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000403 AC: 10AN: 248230Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135068
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1461246Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 726908
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at