rs775761112
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152309.3(PIK3AP1):c.2015-6T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152309.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIK3AP1 | NM_152309.3 | c.2015-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000339364.10 | |||
PIK3AP1 | XM_005269499.2 | c.1481-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PIK3AP1 | XM_011539248.2 | c.2015-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PIK3AP1 | XM_047424566.1 | c.1481-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIK3AP1 | ENST00000339364.10 | c.2015-6T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_152309.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250878Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135618
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461458Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727056
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Infantile spasms Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at