chr1-214364635-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_005401.5(PTPN14):c.3312C>T(p.Asn1104=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000994 in 1,614,104 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0051 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00057 ( 9 hom. )
Consequence
PTPN14
NM_005401.5 synonymous
NM_005401.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.83
Genes affected
PTPN14 (HGNC:9647): (protein tyrosine phosphatase non-receptor type 14) 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 noncatalytic domain similar to that of band 4.1 superfamily cytoskeleton-associated proteins, which suggested the membrane or cytoskeleton localization of this protein. It appears to regulate lymphatic development in mammals, and a loss of function mutation has been found in a kindred with a lymphedema-choanal atresia. [provided by RefSeq, Sep 2010]
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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=-0.34).
BP6
?
Variant 1-214364635-G-A is Benign according to our data. Variant chr1-214364635-G-A is described in ClinVar as [Benign]. Clinvar id is 791232.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-214364635-G-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00507 (772/152226) while in subpopulation AFR AF= 0.0173 (719/41546). AF 95% confidence interval is 0.0163. There are 11 homozygotes in gnomad4. There are 367 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN14 | NM_005401.5 | c.3312C>T | p.Asn1104= | synonymous_variant | 18/19 | ENST00000366956.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN14 | ENST00000366956.10 | c.3312C>T | p.Asn1104= | synonymous_variant | 18/19 | 1 | NM_005401.5 | P1 | |
PTPN14 | ENST00000543945.5 | c.*2588C>T | 3_prime_UTR_variant | 17/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00510 AC: 776AN: 152108Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00149 AC: 374AN: 251140Hom.: 3 AF XY: 0.00105 AC XY: 142AN XY: 135744
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GnomAD4 exome AF: 0.000570 AC: 833AN: 1461878Hom.: 9 Cov.: 31 AF XY: 0.000477 AC XY: 347AN XY: 727244
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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 | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at