9-8331574-A-AAACTTACCATTCTTGAACTGTAACT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002839.4(PTPRD):c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 1,606,216 control chromosomes in the GnomAD database, including 2,441 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.047 ( 209 hom., cov: 0)
Exomes 𝑓: 0.045 ( 2232 hom. )
Consequence
PTPRD
NM_002839.4 splice_region, intron
NM_002839.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.111
Genes affected
PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is Benign according to our data. Variant chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is described in ClinVar as [Benign]. Clinvar id is 227045.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRD | NM_002839.4 | c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region_variant, intron_variant | ENST00000381196.9 | NP_002830.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRD | ENST00000381196.9 | c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region_variant, intron_variant | 5 | NM_002839.4 | ENSP00000370593 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0466 AC: 7082AN: 151890Hom.: 207 Cov.: 0
GnomAD3 genomes
AF:
AC:
7082
AN:
151890
Hom.:
Cov.:
0
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 AF: 0.0449 AC: 65343AN: 1454212Hom.: 2232 Cov.: 35 AF XY: 0.0481 AC XY: 34834AN XY: 723618
GnomAD4 exome
AF:
AC:
65343
AN:
1454212
Hom.:
Cov.:
35
AF XY:
AC XY:
34834
AN XY:
723618
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: 0.0468 AC: 7108AN: 152004Hom.: 209 Cov.: 0 AF XY: 0.0499 AC XY: 3707AN XY: 74300
GnomAD4 genome
AF:
AC:
7108
AN:
152004
Hom.:
Cov.:
0
AF XY:
AC XY:
3707
AN XY:
74300
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 specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 03, 2015 | c.5534+7_5534+8ins25 in intron 44 of PTPRD: This variant is not expected to have clinical significance because it has been identified in 15% (2409/16470) South Asian chromosomes, including 184 homozygotes, by the Exome Aggregation Consortiu m Sequencing Project (http://exac.broadinstitute.org/variant/9-8331574-A-AAACTTA CCATTCTTGAACTGTAACT; dbSNP rs3215098). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at