17-1497972-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_016532.4(INPP5K):c.927C>T(p.Ser309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00243 in 1,614,012 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 48 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 32 hom. )
Consequence
INPP5K
NM_016532.4 synonymous
NM_016532.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
Genes affected
INPP5K (HGNC:33882): (inositol polyphosphate-5-phosphatase K) This gene encodes a protein with 5-phosphatase activity toward polyphosphate inositol. The protein localizes to the cytosol in regions lacking actin stress fibers. It is thought that this protein may negatively regulate the actin cytoskeleton. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 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=-0.48).
BP6
Variant 17-1497972-G-A is Benign according to our data. Variant chr17-1497972-G-A is described in ClinVar as [Benign]. Clinvar id is 789650.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.29 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.013 (1979/152292) while in subpopulation AFR AF= 0.0439 (1824/41534). AF 95% confidence interval is 0.0422. There are 48 homozygotes in gnomad4. There are 941 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 48 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPP5K | NM_016532.4 | c.927C>T | p.Ser309= | synonymous_variant | 8/12 | ENST00000421807.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPP5K | ENST00000421807.7 | c.927C>T | p.Ser309= | synonymous_variant | 8/12 | 1 | NM_016532.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0130 AC: 1974AN: 152174Hom.: 48 Cov.: 33
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GnomAD3 exomes AF: 0.00349 AC: 877AN: 251112Hom.: 26 AF XY: 0.00284 AC XY: 385AN XY: 135738
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GnomAD4 exome AF: 0.00133 AC: 1944AN: 1461720Hom.: 32 Cov.: 31 AF XY: 0.00114 AC XY: 829AN XY: 727172
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GnomAD4 genome AF: 0.0130 AC: 1979AN: 152292Hom.: 48 Cov.: 33 AF XY: 0.0126 AC XY: 941AN XY: 74458
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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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Benign
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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