9-9206006-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002839.4(PTPRD):​c.-202-22643A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,144 control chromosomes in the GnomAD database, including 2,977 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 2977 hom., cov: 32)

Consequence

PTPRD
NM_002839.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.976
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRDNM_002839.4 linkuse as main transcriptc.-202-22643A>C intron_variant ENST00000381196.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRDENST00000381196.9 linkuse as main transcriptc.-202-22643A>C intron_variant 5 NM_002839.4 P1P23468-1
PTPRDENST00000463477.5 linkuse as main transcriptc.-202-22643A>C intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.195
AC:
29690
AN:
152026
Hom.:
2975
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.232
Gnomad AMR
AF:
0.163
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.336
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.177
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.195
AC:
29707
AN:
152144
Hom.:
2977
Cov.:
32
AF XY:
0.197
AC XY:
14680
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.163
Gnomad4 ASJ
AF:
0.206
Gnomad4 EAS
AF:
0.336
Gnomad4 SAS
AF:
0.212
Gnomad4 FIN
AF:
0.239
Gnomad4 NFE
AF:
0.177
Gnomad4 OTH
AF:
0.181
Alfa
AF:
0.190
Hom.:
940
Bravo
AF:
0.192
Asia WGS
AF:
0.262
AC:
913
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.8
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs12685122; hg19: chr9-9206006; API