X-72186506-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006223.4(PIN4):c.89G>T(p.Gly30Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000896 in 111,582 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIN4 | NM_006223.4 | c.89G>T | p.Gly30Val | missense_variant | Exon 2 of 4 | ENST00000373669.8 | NP_006214.3 | |
PIN4 | NM_001170747.1 | c.164G>T | p.Gly55Val | missense_variant | Exon 2 of 4 | NP_001164218.1 | ||
PIN4 | NR_033187.2 | n.72+4678G>T | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111582Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33752
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000184 AC: 2AN: 1086944Hom.: 0 Cov.: 27 AF XY: 0.00000283 AC XY: 1AN XY: 352816
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111582Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33752
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164G>T (p.G55V) alteration is located in exon 2 (coding exon 2) of the PIN4 gene. This alteration results from a G to T substitution at nucleotide position 164, causing the glycine (G) at amino acid position 55 to be replaced by a valine (V). 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