rs2709591
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003887.3(ASAP2):c.1161-17T>C 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 0.58 in 1,613,672 control chromosomes in the GnomAD database, including 281,056 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_003887.3 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 |
---|---|---|---|---|---|---|---|
ASAP2 | NM_003887.3 | c.1161-17T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000281419.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASAP2 | ENST00000281419.8 | c.1161-17T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003887.3 | P3 | |||
ASAP2 | ENST00000315273.4 | c.1161-17T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
ASAP2 | ENST00000641030.1 | c.700-17T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||||
ASAP2 | ENST00000471687.1 | n.487-17T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.646 AC: 98191AN: 151932Hom.: 33929 Cov.: 32
GnomAD3 exomes AF: 0.550 AC: 138197AN: 251370Hom.: 40818 AF XY: 0.550 AC XY: 74696AN XY: 135846
GnomAD4 exome AF: 0.574 AC: 838279AN: 1461622Hom.: 247074 Cov.: 53 AF XY: 0.573 AC XY: 416692AN XY: 727106
GnomAD4 genome AF: 0.647 AC: 98302AN: 152050Hom.: 33982 Cov.: 32 AF XY: 0.639 AC XY: 47471AN XY: 74326
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at