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rs10506598

Variant summary

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

The NM_001109754.4(PTPRB):c.708+231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,066 control chromosomes in the GnomAD database, including 6,303 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 0.28 ( 6303 hom., cov: 32)

Consequence

PTPRB
NM_001109754.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165
Variant links:
Genes affected
PTPRB (HGNC:9665): (protein tyrosine phosphatase receptor type B) 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 domain, a single transmembrane segment and one intracytoplasmic catalytic domain, thus belongs to receptor type PTP. The extracellular region of this PTP is composed of multiple fibronectin type_III repeats, which was shown to interact with neuronal receptor and cell adhesion molecules, such as contactin and tenascin C. This protein was also found to interact with sodium channels, and thus may regulate sodium channels by altering tyrosine phosphorylation status. The functions of the interaction partners of this protein implicate the roles of this PTP in cell adhesion, neurite growth, and neuronal differentiation. Alternate transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

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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 (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTPRBNM_001109754.4 linkuse as main transcriptc.708+231A>G intron_variant ENST00000334414.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTPRBENST00000334414.11 linkuse as main transcriptc.708+231A>G intron_variant 1 NM_001109754.4 A1P23467-3

Frequencies

GnomAD3 genomes
AF:
0.283
AC:
42971
AN:
151948
Hom.:
6288
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.340
Gnomad AMI
AF:
0.111
Gnomad AMR
AF:
0.318
Gnomad ASJ
AF:
0.263
Gnomad EAS
AF:
0.217
Gnomad SAS
AF:
0.297
Gnomad FIN
AF:
0.291
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.247
Gnomad OTH
AF:
0.289
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.283
AC:
43043
AN:
152066
Hom.:
6303
Cov.:
32
AF XY:
0.286
AC XY:
21245
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.340
Gnomad4 AMR
AF:
0.318
Gnomad4 ASJ
AF:
0.263
Gnomad4 EAS
AF:
0.217
Gnomad4 SAS
AF:
0.297
Gnomad4 FIN
AF:
0.291
Gnomad4 NFE
AF:
0.247
Gnomad4 OTH
AF:
0.289
Alfa
AF:
0.258
Hom.:
7377
Bravo
AF:
0.287
Asia WGS
AF:
0.264
AC:
916
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
2.0
Dann
Benign
0.52

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: rs10506598; hg19: chr12-71015939; API