20-42085817-A-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_007050.6(PTPRT):c.3883T>A(p.Cys1295Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,613,620 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007050.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRT | NM_007050.6 | c.3883T>A | p.Cys1295Ser | missense_variant | 28/31 | ENST00000373187.6 | |
LOC101927182 | XR_001754611.2 | n.378-4762A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRT | ENST00000373187.6 | c.3883T>A | p.Cys1295Ser | missense_variant | 28/31 | 1 | NM_007050.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 240AN: 152132Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000401 AC: 100AN: 249448Hom.: 1 AF XY: 0.000222 AC XY: 30AN XY: 135334
GnomAD4 exome AF: 0.000151 AC: 220AN: 1461370Hom.: 2 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 727014
GnomAD4 genome AF: 0.00157 AC: 239AN: 152250Hom.: 1 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74436
ClinVar
Submissions by phenotype
PTPRT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 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