2-60954117-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144709.4(PUS10):c.1099C>T(p.His367Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144709.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PUS10 | NM_144709.4 | c.1099C>T | p.His367Tyr | missense_variant | 13/18 | ENST00000316752.11 | NP_653310.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PUS10 | ENST00000316752.11 | c.1099C>T | p.His367Tyr | missense_variant | 13/18 | 1 | NM_144709.4 | ENSP00000326003 | P1 | |
PUS10 | ENST00000602599.1 | n.3702C>T | non_coding_transcript_exon_variant | 11/16 | 1 | |||||
PUS10 | ENST00000407787.5 | c.1099C>T | p.His367Tyr | missense_variant | 13/18 | 2 | ENSP00000386074 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251412Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135874
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727226
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.1099C>T (p.H367Y) alteration is located in exon 13 (coding exon 12) of the PUS10 gene. This alteration results from a C to T substitution at nucleotide position 1099, causing the histidine (H) at amino acid position 367 to be replaced by a tyrosine (Y). 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