chr15-89793142-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001150.3(ANPEP):c.2158-16A>G 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 0.319 in 1,605,492 control chromosomes in the GnomAD database, including 84,117 homozygotes. 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_001150.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANPEP | NM_001150.3 | c.2158-16A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000300060.7 | |||
ANPEP | NM_001381923.1 | c.2158-16A>G | splice_polypyrimidine_tract_variant, intron_variant | ||||
ANPEP | NM_001381924.1 | c.2158-16A>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANPEP | ENST00000300060.7 | c.2158-16A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001150.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52457AN: 151778Hom.: 9674 Cov.: 31
GnomAD3 exomes AF: 0.300 AC: 75352AN: 250930Hom.: 12022 AF XY: 0.302 AC XY: 40966AN XY: 135652
GnomAD4 exome AF: 0.316 AC: 459812AN: 1453596Hom.: 74421 Cov.: 29 AF XY: 0.317 AC XY: 229056AN XY: 723626
GnomAD4 genome AF: 0.346 AC: 52534AN: 151896Hom.: 9696 Cov.: 31 AF XY: 0.336 AC XY: 24961AN XY: 74230
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at