7-157621372-G-GGCCAGTTTCCACCGCCCGTAACCCAGGCTTCCTGCCCCCGGGGCTGGTACGTACAGGTCAGCACA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002847.5(PTPRN2):c.2333_2334insTGTGCTGACCTGTACGTACCAGCCCCGGGGGCAGGAAGCCTGGGTTACGGGCGGTGGAAACTGGC(p.Tyr782fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 145,058 control chromosomes in the GnomAD database, including 324 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.022 ( 324 hom., cov: 34)
Exomes 𝑓: 0.018 ( 1231 hom. )
Failed GnomAD Quality Control
Consequence
PTPRN2
NM_002847.5 frameshift
NM_002847.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.69
Genes affected
PTPRN2 (HGNC:9677): (protein tyrosine phosphatase receptor type N2) This gene encodes a protein with sequence similarity to receptor-like protein tyrosine phosphatases. However, tyrosine phosphatase activity has not been experimentally validated for this protein. Studies of the rat ortholog suggest that the encoded protein may instead function as a phosphatidylinositol phosphatase with the ability to dephosphorylate phosphatidylinositol 3-phosphate and phosphatidylinositol 4,5-diphosphate, and this function may be involved in the regulation of insulin secretion. This protein has been identified as an autoantigen in insulin-dependent diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 7-157621372-G-GGCCAGTTTCCACCGCCCGTAACCCAGGCTTCCTGCCCCCGGGGCTGGTACGTACAGGTCAGCACA is Benign according to our data. Variant chr7-157621372-G-GGCCAGTTTCCACCGCCCGTAACCCAGGCTTCCTGCCCCCGGGGCTGGTACGTACAGGTCAGCACA is described in ClinVar as [Benign]. Clinvar id is 789293.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0219 (3182/145058) while in subpopulation NFE AF= 0.0303 (1941/64138). AF 95% confidence interval is 0.0291. There are 324 homozygotes in gnomad4. There are 1520 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 324 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0220 AC: 3182AN: 144936Hom.: 324 Cov.: 34
GnomAD3 genomes
AF:
AC:
3182
AN:
144936
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0184 AC: 25816AN: 1402188Hom.: 1231 Cov.: 36 AF XY: 0.0189 AC XY: 13201AN XY: 698560
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
25816
AN:
1402188
Hom.:
Cov.:
36
AF XY:
AC XY:
13201
AN XY:
698560
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0219 AC: 3182AN: 145058Hom.: 324 Cov.: 34 AF XY: 0.0214 AC XY: 1520AN XY: 70984
GnomAD4 genome
AF:
AC:
3182
AN:
145058
Hom.:
Cov.:
34
AF XY:
AC XY:
1520
AN XY:
70984
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at