chr3-61562327-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002841.4(PTPRG):c.40C>T(p.Leu14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00252 in 1,613,682 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 45 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 39 hom. )
Consequence
PTPRG
NM_002841.4 synonymous
NM_002841.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.70
Genes affected
PTPRG (HGNC:9671): (protein tyrosine phosphatase receptor type G) 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 possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this PTP contains a carbonic anhydrase-like (CAH) domain, which is also found in the extracellular region of PTPRBETA/ZETA. This gene is located in a chromosomal region that is frequently deleted in renal cell carcinoma and lung carcinoma, thus is thought to be a candidate tumor suppressor gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 3-61562327-C-T is Benign according to our data. Variant chr3-61562327-C-T is described in ClinVar as [Benign]. Clinvar id is 708655.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.7 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0137 (2085/152232) while in subpopulation AFR AF= 0.0471 (1959/41554). AF 95% confidence interval is 0.0454. There are 45 homozygotes in gnomad4. There are 1000 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRG | NM_002841.4 | c.40C>T | p.Leu14= | synonymous_variant | 1/30 | ENST00000474889.6 | |
PTPRG | NM_001375471.1 | c.40C>T | p.Leu14= | synonymous_variant | 1/29 | ||
PTPRG | XM_017006961.2 | c.40C>T | p.Leu14= | synonymous_variant | 1/31 | ||
PTPRG | XM_017006963.2 | c.40C>T | p.Leu14= | synonymous_variant | 1/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRG | ENST00000474889.6 | c.40C>T | p.Leu14= | synonymous_variant | 1/30 | 1 | NM_002841.4 | A1 | |
PTPRG | ENST00000295874.14 | c.40C>T | p.Leu14= | synonymous_variant | 1/29 | 1 | P4 | ||
PTPRG | ENST00000495879.1 | n.759C>T | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
PTPRG | ENST00000475527.1 | n.477C>T | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0137 AC: 2083AN: 152114Hom.: 45 Cov.: 32
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GnomAD3 exomes AF: 0.00359 AC: 900AN: 250548Hom.: 18 AF XY: 0.00245 AC XY: 332AN XY: 135522
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GnomAD4 exome AF: 0.00136 AC: 1989AN: 1461450Hom.: 39 Cov.: 31 AF XY: 0.00113 AC XY: 820AN XY: 727058
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at