rs2302224
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002850.4(PTPRS):c.5362-17C>T 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 0.258 in 1,613,776 control chromosomes in the GnomAD database, including 55,393 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. There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_002850.4 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 |
---|---|---|---|---|---|---|---|
PTPRS | NM_002850.4 | c.5362-17C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000262963.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRS | ENST00000262963.11 | c.5362-17C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_002850.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42815AN: 152020Hom.: 6193 Cov.: 33
GnomAD3 exomes AF: 0.265 AC: 66490AN: 250588Hom.: 9493 AF XY: 0.261 AC XY: 35421AN XY: 135504
GnomAD4 exome AF: 0.255 AC: 373392AN: 1461638Hom.: 49193 Cov.: 35 AF XY: 0.254 AC XY: 185023AN XY: 727098
GnomAD4 genome ? AF: 0.282 AC: 42847AN: 152138Hom.: 6200 Cov.: 33 AF XY: 0.281 AC XY: 20891AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at