chr2-98554381-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001134225.2(INPP4A):c.1458T>C(p.Thr486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000833 in 1,613,742 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00080 ( 19 hom. )
Consequence
INPP4A
NM_001134225.2 synonymous
NM_001134225.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
Genes affected
INPP4A (HGNC:6074): (inositol polyphosphate-4-phosphatase type I A) This gene encodes an Mg++ independent enzyme that hydrolyzes the 4-position phosphate from the inositol ring of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4-trisphosphate, and inositol 3,4-bisphosphate. Multiple transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Aug 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=-0.9).
BP6
?
Variant 2-98554381-T-C is Benign according to our data. Variant chr2-98554381-T-C is described in ClinVar as [Benign]. Clinvar id is 719006.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.32 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00111 (169/152266) while in subpopulation EAS AF= 0.0291 (151/5182). AF 95% confidence interval is 0.0254. There are 2 homozygotes in gnomad4. There are 101 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPP4A | NM_001134225.2 | c.1458T>C | p.Thr486= | synonymous_variant | 15/25 | ENST00000409851.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPP4A | ENST00000409851.8 | c.1458T>C | p.Thr486= | synonymous_variant | 15/25 | 1 | NM_001134225.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00111 AC: 169AN: 152148Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00259 AC: 645AN: 248708Hom.: 13 AF XY: 0.00239 AC XY: 322AN XY: 134972
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GnomAD4 exome AF: 0.000805 AC: 1176AN: 1461476Hom.: 19 Cov.: 31 AF XY: 0.000754 AC XY: 548AN XY: 726990
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GnomAD4 genome ? AF: 0.00111 AC: 169AN: 152266Hom.: 2 Cov.: 33 AF XY: 0.00136 AC XY: 101AN XY: 74468
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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