rs10521693
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005032.7(PLS3):c.-9+4919A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 112,168 control chromosomes in the GnomAD database, including 30 homozygotes. There are 804 hemizygotes in GnomAD. 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_005032.7 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 |
---|---|---|---|---|---|---|---|
PLS3 | NM_005032.7 | c.-9+4919A>C | intron_variant | ENST00000355899.8 | |||
PLS3 | NM_001282337.2 | c.-194+4919A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS3 | ENST00000355899.8 | c.-9+4919A>C | intron_variant | 1 | NM_005032.7 | P1 | |||
PLS3 | ENST00000489283.5 | c.-9+4919A>C | intron_variant, NMD_transcript_variant | 1 | |||||
PLS3 | ENST00000289290.7 | c.-194+4919A>C | intron_variant | 2 | |||||
PLS3 | ENST00000626746.2 | c.-9+4919A>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0245 AC: 2744AN: 112115Hom.: 30 Cov.: 24 AF XY: 0.0234 AC XY: 803AN XY: 34271
GnomAD4 genome ? AF: 0.0245 AC: 2745AN: 112168Hom.: 30 Cov.: 24 AF XY: 0.0234 AC XY: 804AN XY: 34334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at