chr14-88479169-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_007039.4(PTPN21):c.2262C>T(p.Pro754=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,551,738 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 17 hom. )
Consequence
PTPN21
NM_007039.4 synonymous
NM_007039.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0170
Genes affected
PTPN21 (HGNC:9651): (protein tyrosine phosphatase non-receptor type 21) 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 N-terminal domain, similar to cytoskeletal- associated proteins including band 4.1, ezrin, merlin, and radixin. This PTP was shown to specially interact with BMX/ETK, a member of Tec tyrosine kinase family characterized by a multimodular structures including PH, SH3, and SH2 domains. The interaction of this PTP with BMX kinase was found to increase the activation of STAT3, but not STAT2 kinase. Studies of the similar gene in mice suggested the possible roles of this PTP in liver regeneration and spermatogenesis. [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=-0.58).
BP6
?
Variant 14-88479169-G-A is Benign according to our data. Variant chr14-88479169-G-A is described in ClinVar as [Benign]. Clinvar id is 768671.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.017 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1541/152300) while in subpopulation AFR AF= 0.0354 (1471/41568). AF 95% confidence interval is 0.0339. There are 12 homozygotes in gnomad4. There are 705 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN21 | NM_007039.4 | c.2262C>T | p.Pro754= | synonymous_variant | 13/19 | ENST00000556564.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN21 | ENST00000556564.6 | c.2262C>T | p.Pro754= | synonymous_variant | 13/19 | 1 | NM_007039.4 | P1 | |
PTPN21 | ENST00000328736.7 | c.2262C>T | p.Pro754= | synonymous_variant | 12/18 | 1 | P1 | ||
PTPN21 | ENST00000554270.5 | n.2375C>T | non_coding_transcript_exon_variant | 12/17 | 1 | ||||
PTPN21 | ENST00000536337.5 | c.*2199C>T | 3_prime_UTR_variant, NMD_transcript_variant | 13/19 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1534AN: 152182Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00286 AC: 550AN: 192368Hom.: 4 AF XY: 0.00214 AC XY: 222AN XY: 103918
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GnomAD4 exome AF: 0.000933 AC: 1305AN: 1399438Hom.: 17 Cov.: 31 AF XY: 0.000828 AC XY: 572AN XY: 691102
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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 | Apr 04, 2018 | - - |
Computational scores
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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