18-7955114-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001105244.2(PTPRM):c.839-7C>G 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 0.0000486 in 1,584,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001105244.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRM | NM_001105244.2 | c.839-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000580170.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRM | ENST00000580170.6 | c.839-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001105244.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000959 AC: 23AN: 239786Hom.: 0 AF XY: 0.0000772 AC XY: 10AN XY: 129540
GnomAD4 exome AF: 0.0000461 AC: 66AN: 1432754Hom.: 0 Cov.: 31 AF XY: 0.0000466 AC XY: 33AN XY: 707892
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74332
ClinVar
Submissions by phenotype
PTPRM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at