X-72197408-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_006223.4(PIN4):c.278C>A(p.Pro93Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,205,827 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006223.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIN4 | NM_006223.4 | c.278C>A | p.Pro93Gln | missense_variant | Exon 4 of 4 | ENST00000373669.8 | NP_006214.3 | |
PIN4 | NM_001170747.1 | c.312+504C>A | intron_variant | Intron 3 of 3 | NP_001164218.1 | |||
PIN4 | NR_033187.2 | n.233C>A | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111867Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34043
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 177338Hom.: 0 AF XY: 0.0000161 AC XY: 1AN XY: 62216
GnomAD4 exome AF: 0.0000201 AC: 22AN: 1093960Hom.: 0 Cov.: 28 AF XY: 0.0000167 AC XY: 6AN XY: 359566
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111867Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34043
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.353C>A (p.P118Q) alteration is located in exon 4 (coding exon 4) of the PIN4 gene. This alteration results from a C to A substitution at nucleotide position 353, causing the proline (P) at amino acid position 118 to be replaced by a glutamine (Q). 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