chr15-76995578-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003978.5(PSTPIP1):āc.5T>Cā(p.Met2Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M2I) has been classified as Uncertain significance.
Frequency
Consequence
NM_003978.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSTPIP1 | NM_003978.5 | c.5T>C | p.Met2Thr | missense_variant | 1/15 | ENST00000558012.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSTPIP1 | ENST00000558012.6 | c.5T>C | p.Met2Thr | missense_variant | 1/15 | 1 | NM_003978.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000298 AC: 74AN: 248334Hom.: 0 AF XY: 0.000237 AC XY: 32AN XY: 134818
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461516Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 727040
GnomAD4 genome AF: 0.000144 AC: 22AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74480
ClinVar
Submissions by phenotype
Autoinflammatory syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 17, 2021 | - - |
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at