rs2270993
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002843.4(PTPRJ):c.618G>A(p.Glu206Glu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,611,380 control chromosomes in the GnomAD database, including 16,856 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_002843.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRJ | NM_002843.4 | c.618G>A | p.Glu206Glu | splice_region_variant, synonymous_variant | Exon 5 of 25 | ENST00000418331.7 | NP_002834.3 | |
PTPRJ | NM_001098503.2 | c.618G>A | p.Glu206Glu | splice_region_variant, synonymous_variant | Exon 5 of 9 | NP_001091973.1 | ||
PTPRJ | XM_017018085.2 | c.570G>A | p.Glu190Glu | splice_region_variant, synonymous_variant | Exon 5 of 25 | XP_016873574.1 | ||
PTPRJ | XM_047427374.1 | c.960G>A | p.Glu320Glu | splice_region_variant, synonymous_variant | Exon 5 of 17 | XP_047283330.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRJ | ENST00000418331.7 | c.618G>A | p.Glu206Glu | splice_region_variant, synonymous_variant | Exon 5 of 25 | 1 | NM_002843.4 | ENSP00000400010.2 | ||
PTPRJ | ENST00000440289.6 | c.618G>A | p.Glu206Glu | splice_region_variant, synonymous_variant | Exon 5 of 9 | 1 | ENSP00000409733.2 | |||
PTPRJ | ENST00000698881.1 | c.960G>A | p.Glu320Glu | splice_region_variant, synonymous_variant | Exon 5 of 25 | ENSP00000514003.1 | ||||
PTPRJ | ENST00000527952.1 | c.354G>A | p.Glu118Glu | splice_region_variant, synonymous_variant | Exon 4 of 4 | 5 | ENSP00000435618.1 |
Frequencies
GnomAD3 genomes AF: 0.164 AC: 24849AN: 151960Hom.: 2320 Cov.: 32
GnomAD3 exomes AF: 0.140 AC: 35053AN: 250092Hom.: 2663 AF XY: 0.138 AC XY: 18592AN XY: 135214
GnomAD4 exome AF: 0.137 AC: 200356AN: 1459302Hom.: 14534 Cov.: 31 AF XY: 0.136 AC XY: 99023AN XY: 725820
GnomAD4 genome AF: 0.163 AC: 24859AN: 152078Hom.: 2322 Cov.: 32 AF XY: 0.164 AC XY: 12226AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at