rs3215098
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGT
- chr9-8331574-A-AAACTTACCCTTCTTGAACTGTAACT
- chr9-8331574-A-AAACTTACCATTATTCACAAATGGAAACTTACCATTCTTGAACTGT
- chr9-8331574-A-AAACTTACCATTCATGAACTGT
- chr9-8331574-A-AAACTTACCATTCCGAAACTTACCATTCCTGAACTGT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACTT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACTTACCTGCAAGT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACTTACGT
- chr9-8331574-A-AAACTTACCATTCTCGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTCAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTAT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGAAACTTACCATTCTTGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACTAACT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACTTACCTGCAATGGACTGAAGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACTTACCTGCAATGTTGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACTTACGT
- chr9-8331574-A-AAACTTACCATTCTTGAATTGT
- chr9-8331574-A-AAACTTACCATTGTTGAACTGT
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002839.4(PTPRD):c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 1,606,216 control chromosomes in the GnomAD database, including 2,441 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.047 ( 209 hom., cov: 0)
Exomes 𝑓: 0.045 ( 2232 hom. )
Consequence
PTPRD
NM_002839.4 splice_region, intron
NM_002839.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.111
Publications
3 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is Benign according to our data. Variant chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT is described in ClinVar as Benign. ClinVar VariationId is 227045.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002839.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PTPRD | MANE Select | c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | NP_002830.1 | P23468-1 | |||
| PTPRD | c.5594+7_5594+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | NP_001364887.1 | |||||
| PTPRD | c.5549+7_5549+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | NP_001364987.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PTPRD | TSL:5 MANE Select | c.5534+7_5534+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | ENSP00000370593.3 | P23468-1 | |||
| PTPRD | TSL:1 | c.4316+7_4316+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | ENSP00000347373.5 | P23468-6 | |||
| PTPRD | TSL:1 | c.4313+7_4313+8insAGTTACAGTTCAAGAATGGTAAGTT | splice_region intron | N/A | ENSP00000380731.3 | P23468-4 |
Frequencies
GnomAD3 genomes 0.0466 AC: 7082AN: 151890Hom.: 207 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
7082
AN:
151890
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0449 AC: 65343AN: 1454212Hom.: 2232 Cov.: 35 AF XY: 0.0481 AC XY: 34834AN XY: 723618 show subpopulations
GnomAD4 exome
AF:
AC:
65343
AN:
1454212
Hom.:
Cov.:
35
AF XY:
AC XY:
34834
AN XY:
723618
show subpopulations
African (AFR)
AF:
AC:
1353
AN:
33392
American (AMR)
AF:
AC:
2423
AN:
44584
Ashkenazi Jewish (ASJ)
AF:
AC:
874
AN:
26094
East Asian (EAS)
AF:
AC:
1371
AN:
39610
South Asian (SAS)
AF:
AC:
11955
AN:
85800
European-Finnish (FIN)
AF:
AC:
2504
AN:
53144
Middle Eastern (MID)
AF:
AC:
455
AN:
5734
European-Non Finnish (NFE)
AF:
AC:
41357
AN:
1105766
Other (OTH)
AF:
AC:
3051
AN:
60088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.403
Heterozygous variant carriers
0
2059
4117
6176
8234
10293
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1572
3144
4716
6288
7860
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0468 AC: 7108AN: 152004Hom.: 209 Cov.: 0 AF XY: 0.0499 AC XY: 3707AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
7108
AN:
152004
Hom.:
Cov.:
0
AF XY:
AC XY:
3707
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
1769
AN:
41428
American (AMR)
AF:
AC:
791
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
136
AN:
3472
East Asian (EAS)
AF:
AC:
161
AN:
5162
South Asian (SAS)
AF:
AC:
750
AN:
4816
European-Finnish (FIN)
AF:
AC:
497
AN:
10586
Middle Eastern (MID)
AF:
AC:
17
AN:
294
European-Non Finnish (NFE)
AF:
AC:
2846
AN:
67976
Other (OTH)
AF:
AC:
105
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.494
Heterozygous variant carriers
0
318
636
955
1273
1591
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
88
176
264
352
440
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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