2-21033533-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000384.3(APOB):c.905-15C>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,603,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000384.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOB | NM_000384.3 | c.905-15C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000233242.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOB | ENST00000233242.5 | c.905-15C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000384.3 | P1 | |||
APOB | ENST00000399256.4 | c.905-15C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
APOB | ENST00000673739.2 | c.*211-15C>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | ||||||
APOB | ENST00000673882.2 | c.*211-15C>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450846Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 722518
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at