10-98392439-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032709.3(PYROXD2):c.1055C>T(p.Thr352Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,613,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032709.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYROXD2 | NM_032709.3 | c.1055C>T | p.Thr352Met | missense_variant | 10/16 | ENST00000370575.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYROXD2 | ENST00000370575.5 | c.1055C>T | p.Thr352Met | missense_variant | 10/16 | 1 | NM_032709.3 | P1 | |
PYROXD2 | ENST00000483923.5 | n.1957C>T | non_coding_transcript_exon_variant | 10/15 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250678Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135522
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461174Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 726938
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.1055C>T (p.T352M) alteration is located in exon 10 (coding exon 10) of the PYROXD2 gene. This alteration results from a C to T substitution at nucleotide position 1055, causing the threonine (T) at amino acid position 352 to be replaced by a methionine (M). 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