X-72181798-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006223.4(PIN4):c.13G>A(p.Gly5Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000038 in 1,183,531 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIN4 | NM_006223.4 | c.13G>A | p.Gly5Arg | missense_variant | Exon 1 of 4 | ENST00000373669.8 | NP_006214.3 | |
PIN4 | NM_001170747.1 | c.88G>A | p.Gly30Arg | missense_variant | Exon 1 of 4 | NP_001164218.1 | ||
PIN4 | NR_033187.2 | n.42G>A | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 6AN: 112021Hom.: 0 Cov.: 24 AF XY: 0.0000293 AC XY: 1AN XY: 34183
GnomAD3 exomes AF: 0.0000575 AC: 10AN: 173899Hom.: 0 AF XY: 0.0000842 AC XY: 5AN XY: 59395
GnomAD4 exome AF: 0.0000364 AC: 39AN: 1071510Hom.: 0 Cov.: 27 AF XY: 0.0000648 AC XY: 22AN XY: 339248
GnomAD4 genome AF: 0.0000536 AC: 6AN: 112021Hom.: 0 Cov.: 24 AF XY: 0.0000293 AC XY: 1AN XY: 34183
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.88G>A (p.G30R) alteration is located in exon 1 (coding exon 1) of the PIN4 gene. This alteration results from a G to A substitution at nucleotide position 88, causing the glycine (G) at amino acid position 30 to be replaced by an arginine (R). 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