2-98544045-GCACACACA-GCACACACACACACA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001134225.2(INPP4A):c.949+52_949+57dupACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000902 in 1,441,472 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 24)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
INPP4A
NM_001134225.2 intron
NM_001134225.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.72
Publications
4 publications found
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]
INPP4A Gene-Disease associations (from GenCC):
- neurodevelopmental disorderInheritance: AR Classification: LIMITED Submitted by: G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000332 AC: 5AN: 150412Hom.: 0 Cov.: 24 show subpopulations
GnomAD3 genomes
AF:
AC:
5
AN:
150412
Hom.:
Cov.:
24
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000620 AC: 8AN: 1291060Hom.: 0 Cov.: 0 AF XY: 0.00000471 AC XY: 3AN XY: 636348 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
1291060
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
636348
show subpopulations
African (AFR)
AF:
AC:
3
AN:
29574
American (AMR)
AF:
AC:
0
AN:
33538
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23022
East Asian (EAS)
AF:
AC:
0
AN:
33562
South Asian (SAS)
AF:
AC:
0
AN:
73084
European-Finnish (FIN)
AF:
AC:
0
AN:
43828
Middle Eastern (MID)
AF:
AC:
0
AN:
5154
European-Non Finnish (NFE)
AF:
AC:
5
AN:
995706
Other (OTH)
AF:
AC:
0
AN:
53592
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000332 AC: 5AN: 150412Hom.: 0 Cov.: 24 AF XY: 0.0000136 AC XY: 1AN XY: 73382 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
150412
Hom.:
Cov.:
24
AF XY:
AC XY:
1
AN XY:
73382
show subpopulations
African (AFR)
AF:
AC:
3
AN:
40728
American (AMR)
AF:
AC:
0
AN:
15130
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3452
East Asian (EAS)
AF:
AC:
1
AN:
5144
South Asian (SAS)
AF:
AC:
0
AN:
4762
European-Finnish (FIN)
AF:
AC:
0
AN:
10320
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67588
Other (OTH)
AF:
AC:
0
AN:
2066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.445
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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