rs999890
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_015040.4(PIKFYVE):c.3097T>A(p.Ser1033Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015040.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIKFYVE | NM_015040.4 | c.3097T>A | p.Ser1033Thr | missense_variant | 20/42 | ENST00000264380.9 | NP_055855.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIKFYVE | ENST00000264380.9 | c.3097T>A | p.Ser1033Thr | missense_variant | 20/42 | 1 | NM_015040.4 | ENSP00000264380.4 | ||
PIKFYVE | ENST00000443896.5 | n.*2448T>A | non_coding_transcript_exon_variant | 19/19 | 1 | ENSP00000407692.1 | ||||
PIKFYVE | ENST00000443896.5 | n.*2448T>A | 3_prime_UTR_variant | 19/19 | 1 | ENSP00000407692.1 | ||||
PIKFYVE | ENST00000452564.1 | c.2929T>A | p.Ser977Thr | missense_variant | 19/25 | 2 | ENSP00000405736.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251002Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135640
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461676Hom.: 0 Cov.: 74 AF XY: 0.00000413 AC XY: 3AN XY: 727150
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at