9-8331574-A-AAACTTACTTACCATTCTTGAACTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_002839.4(PTPRD):​c.5534+7_5534+8insACAGTTCAAGAATGGTAAGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.013 ( 42 hom., cov: 0)
Exomes 𝑓: 0.0014 ( 56 hom. )
Failed GnomAD Quality Control

Consequence

PTPRD
NM_002839.4 splice_region, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.111
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 9-8331574-A-AAACTTACTTACCATTCTTGAACTGT is Benign according to our data. Variant chr9-8331574-A-AAACTTACTTACCATTCTTGAACTGT is described in ClinVar as [Likely_benign]. Clinvar id is 2504285.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0129 (1966/152024) while in subpopulation AFR AF= 0.0439 (1817/41426). AF 95% confidence interval is 0.0422. There are 42 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1966 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTPRDNM_002839.4 linkuse as main transcriptc.5534+7_5534+8insACAGTTCAAGAATGGTAAGTAAGTT splice_region_variant, intron_variant ENST00000381196.9 NP_002830.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTPRDENST00000381196.9 linkuse as main transcriptc.5534+7_5534+8insACAGTTCAAGAATGGTAAGTAAGTT splice_region_variant, intron_variant 5 NM_002839.4 ENSP00000370593 P1P23468-1

Frequencies

GnomAD3 genomes
AF:
0.0129
AC:
1959
AN:
151908
Hom.:
43
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0438
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00741
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00913
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00143
AC:
2084
AN:
1460110
Hom.:
56
Cov.:
35
AF XY:
0.00121
AC XY:
877
AN XY:
726472
show subpopulations
Gnomad4 AFR exome
AF:
0.0481
Gnomad4 AMR exome
AF:
0.00379
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000813
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.0000954
Gnomad4 OTH exome
AF:
0.00302
GnomAD4 genome
AF:
0.0129
AC:
1966
AN:
152024
Hom.:
42
Cov.:
0
AF XY:
0.0122
AC XY:
909
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.0439
Gnomad4 AMR
AF:
0.00740
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00903
Alfa
AF:
0.000567
Hom.:
0
Bravo
AF:
0.0148

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 07, 2023See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs368394000; hg19: chr9-8331574; API