rs598356

Positions:

Variant summary

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

The NM_002839.4(PTPRD):​c.-286-14043A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,746 control chromosomes in the GnomAD database, including 7,876 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 0.31 ( 7876 hom., cov: 32)

Consequence

PTPRD
NM_002839.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0510
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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRDNM_002839.4 linkuse as main transcriptc.-286-14043A>C intron_variant ENST00000381196.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRDENST00000381196.9 linkuse as main transcriptc.-286-14043A>C intron_variant 5 NM_002839.4 P1P23468-1
PTPRDENST00000463477.5 linkuse as main transcriptc.-358-14043A>C intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.313
AC:
47497
AN:
151628
Hom.:
7872
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.252
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.181
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.407
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.365
Gnomad OTH
AF:
0.314
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.313
AC:
47526
AN:
151746
Hom.:
7876
Cov.:
32
AF XY:
0.311
AC XY:
23042
AN XY:
74142
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.252
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.180
Gnomad4 SAS
AF:
0.152
Gnomad4 FIN
AF:
0.407
Gnomad4 NFE
AF:
0.365
Gnomad4 OTH
AF:
0.316
Alfa
AF:
0.335
Hom.:
3685
Bravo
AF:
0.300
Asia WGS
AF:
0.202
AC:
696
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.6
DANN
Benign
0.41

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: rs598356; hg19: chr9-9588824; COSMIC: COSV67064896; API