chr19-9835366-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_006221.4(PIN1):c.22C>T(p.Pro8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000046 in 1,522,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P8L) has been classified as Uncertain significance.
Frequency
Consequence
NM_006221.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIN1 | NM_006221.4 | c.22C>T | p.Pro8Ser | missense_variant | 1/4 | ENST00000247970.9 | |
PIN1 | XM_011528068.3 | c.-81C>T | 5_prime_UTR_variant | 1/6 | |||
PIN1 | NR_038422.3 | n.49C>T | non_coding_transcript_exon_variant | 1/5 | |||
PIN1 | NR_038830.2 | n.49C>T | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIN1 | ENST00000247970.9 | c.22C>T | p.Pro8Ser | missense_variant | 1/4 | 1 | NM_006221.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000842 AC: 1AN: 118770Hom.: 0 AF XY: 0.0000153 AC XY: 1AN XY: 65450
GnomAD4 exome AF: 0.00000292 AC: 4AN: 1370396Hom.: 0 Cov.: 31 AF XY: 0.00000444 AC XY: 3AN XY: 676216
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.22C>T (p.P8S) alteration is located in exon 1 (coding exon 1) of the PIN1 gene. This alteration results from a C to T substitution at nucleotide position 22, causing the proline (P) at amino acid position 8 to be replaced by a serine (S). 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