7-157576606-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002847.5(PTPRN2):c.2783+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,606,004 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_002847.5 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRN2 | NM_002847.5 | c.2783+7C>T | splice_region_variant, intron_variant | ENST00000389418.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRN2 | ENST00000389418.9 | c.2783+7C>T | splice_region_variant, intron_variant | 1 | NM_002847.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000788 AC: 120AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000228 AC: 54AN: 236762Hom.: 1 AF XY: 0.000163 AC XY: 21AN XY: 128776
GnomAD4 exome AF: 0.000100 AC: 146AN: 1453684Hom.: 1 Cov.: 30 AF XY: 0.0000844 AC XY: 61AN XY: 722414
GnomAD4 genome AF: 0.000788 AC: 120AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at