rs13108061
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152683.4(PRIMPOL):c.-59-7G>T 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 0.559 in 1,201,306 control chromosomes in the GnomAD database, including 192,960 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_152683.4 splice_region, 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 |
---|---|---|---|---|---|---|---|
PRIMPOL | NM_152683.4 | c.-59-7G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000314970.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRIMPOL | ENST00000314970.11 | c.-59-7G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_152683.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.481 AC: 73129AN: 151922Hom.: 18801 Cov.: 33
GnomAD4 exome AF: 0.571 AC: 598726AN: 1049266Hom.: 174160 Cov.: 13 AF XY: 0.569 AC XY: 294001AN XY: 517146
GnomAD4 genome ? AF: 0.481 AC: 73135AN: 152040Hom.: 18800 Cov.: 33 AF XY: 0.478 AC XY: 35541AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at