GeneBe

12-70555053-A-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001109754.4(PTPRB):​c.5143+107T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PTPRB
NM_001109754.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.264

Publications

4 publications found
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001109754.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PTPRB
NM_001109754.4
MANE Select
c.5143+107T>A
intron
N/ANP_001103224.1
PTPRB
NM_001330204.2
c.4879+107T>A
intron
N/ANP_001317133.1
PTPRB
NM_002837.6
c.4489+107T>A
intron
N/ANP_002828.3

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PTPRB
ENST00000334414.11
TSL:1 MANE Select
c.5143+107T>A
intron
N/AENSP00000334928.6
PTPRB
ENST00000261266.9
TSL:1
c.4489+107T>A
intron
N/AENSP00000261266.5
PTPRB
ENST00000538708.5
TSL:1
c.4219+107T>A
intron
N/AENSP00000438927.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1174016
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
583606
African (AFR)
AF:
0.00
AC:
0
AN:
25950
American (AMR)
AF:
0.00
AC:
0
AN:
26804
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
18876
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36412
South Asian (SAS)
AF:
0.00
AC:
0
AN:
64554
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48334
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4174
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
899016
Other (OTH)
AF:
0.00
AC:
0
AN:
49896
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
5.3
DANN
Benign
0.87
PhyloP100
-0.26

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

Other links and lift over

dbSNP: rs2278342; hg19: chr12-70948833; API