15-76995579-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000558012.6(PSTPIP1):c.6G>T(p.Met2Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign 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. M2T) has been classified as Likely benign.
Frequency
Consequence
ENST00000558012.6 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSTPIP1 | NM_003978.5 | c.6G>T | p.Met2Ile | missense_variant | 1/15 | ENST00000558012.6 | NP_003969.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSTPIP1 | ENST00000558012.6 | c.6G>T | p.Met2Ile | missense_variant | 1/15 | 1 | NM_003978.5 | ENSP00000452746 | P3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248306Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134808
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.6G>T (p.M2I) alteration is located in exon 1 (coding exon 1) of the PSTPIP1 gene. This alteration results from a G to T substitution at nucleotide position 6, causing the methionine (M) at amino acid position 2 to be replaced by an isoleucine (I). 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