ENST00000359785.10:c.1895-32T>C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000359785.10(PTPN22):c.1895-32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 1,592,586 control chromosomes in the GnomAD database, including 446,079 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
ENST00000359785.10 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1895-32T>C | intron_variant | Intron 14 of 20 | NP_057051.4 | |||
PTPN22 | NM_001308297.2 | c.1823-32T>C | intron_variant | Intron 13 of 19 | NP_001295226.2 | |||
PTPN22 | NM_001193431.3 | c.1895-32T>C | intron_variant | Intron 14 of 20 | NP_001180360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.1895-32T>C | intron_variant | Intron 14 of 20 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes AF: 0.767 AC: 116677AN: 152040Hom.: 45698 Cov.: 33
GnomAD3 exomes AF: 0.703 AC: 175823AN: 250146Hom.: 64072 AF XY: 0.712 AC XY: 96301AN XY: 135284
GnomAD4 exome AF: 0.741 AC: 1067643AN: 1440428Hom.: 400327 Cov.: 31 AF XY: 0.742 AC XY: 532848AN XY: 717698
GnomAD4 genome AF: 0.768 AC: 116792AN: 152158Hom.: 45752 Cov.: 33 AF XY: 0.761 AC XY: 56589AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at