chr19-9835367-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_006221.4(PIN1):c.23C>T(p.Pro8Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00011 in 1,521,278 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. P8S) has been classified as Uncertain significance.
Frequency
Consequence
NM_006221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIN1 | NM_006221.4 | c.23C>T | p.Pro8Leu | missense_variant | 1/4 | ENST00000247970.9 | |
PIN1 | XM_011528068.3 | c.-80C>T | 5_prime_UTR_variant | 1/6 | |||
PIN1 | NR_038422.3 | n.50C>T | non_coding_transcript_exon_variant | 1/5 | |||
PIN1 | NR_038830.2 | n.50C>T | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIN1 | ENST00000247970.9 | c.23C>T | p.Pro8Leu | missense_variant | 1/4 | 1 | NM_006221.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 151980Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000339 AC: 4AN: 117886Hom.: 0 AF XY: 0.0000462 AC XY: 3AN XY: 64990
GnomAD4 exome AF: 0.000108 AC: 148AN: 1369298Hom.: 0 Cov.: 31 AF XY: 0.000101 AC XY: 68AN XY: 675660
GnomAD4 genome ? AF: 0.000132 AC: 20AN: 151980Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5AN XY: 74238
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.23C>T (p.P8L) 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 23, causing the proline (P) at amino acid position 8 to be replaced by a leucine (L). 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