10-133380200-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152911.4(PAOX):c.383C>T(p.Ala128Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152911.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAOX | ENST00000278060.10 | c.383C>T | p.Ala128Val | missense_variant | Exon 2 of 7 | 1 | NM_152911.4 | ENSP00000278060.5 | ||
ENSG00000254536 | ENST00000468317.3 | n.-5C>T | non_coding_transcript_exon_variant | Exon 1 of 16 | 5 | ENSP00000436767.2 | ||||
ENSG00000254536 | ENST00000670407.1 | n.-5C>T | non_coding_transcript_exon_variant | Exon 1 of 7 | ENSP00000499264.1 | |||||
ENSG00000254536 | ENST00000468317.3 | n.-5C>T | 5_prime_UTR_variant | Exon 1 of 16 | 5 | ENSP00000436767.2 | ||||
ENSG00000254536 | ENST00000670407.1 | n.-5C>T | 5_prime_UTR_variant | Exon 1 of 7 | ENSP00000499264.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152198Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248876Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135220
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460192Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726336
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152198Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.383C>T (p.A128V) alteration is located in exon 2 (coding exon 2) of the PAOX gene. This alteration results from a C to T substitution at nucleotide position 383, causing the alanine (A) at amino acid position 128 to be replaced by a valine (V). 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