chr14-101882276-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001352913.2(PPP2R5C):c.570+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,602,094 control chromosomes in the GnomAD database, including 240 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001352913.2 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5C | NM_001352913.2 | c.570+5C>T | splice_donor_5th_base_variant, intron_variant | ENST00000694906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5C | ENST00000694906.1 | c.570+5C>T | splice_donor_5th_base_variant, intron_variant | NM_001352913.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0212 AC: 3222AN: 152086Hom.: 112 Cov.: 33
GnomAD3 exomes AF: 0.00564 AC: 1386AN: 245646Hom.: 42 AF XY: 0.00391 AC XY: 519AN XY: 132720
GnomAD4 exome AF: 0.00227 AC: 3291AN: 1449890Hom.: 124 Cov.: 29 AF XY: 0.00199 AC XY: 1435AN XY: 721632
GnomAD4 genome AF: 0.0213 AC: 3239AN: 152204Hom.: 116 Cov.: 33 AF XY: 0.0200 AC XY: 1488AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at