rs9369640
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030948.6(PHACTR1):c.250+151419C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,940 control chromosomes in the GnomAD database, including 26,121 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.57 ( 26121 hom., cov: 32)
Consequence
PHACTR1
NM_030948.6 intron
NM_030948.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.867
Publications
47 publications found
Genes affected
PHACTR1 (HGNC:20990): (phosphatase and actin regulator 1) The protein encoded by this gene is a member of the phosphatase and actin regulator family of proteins. This family member can bind actin and regulate the reorganization of the actin cytoskeleton. It plays a role in tubule formation and in endothelial cell survival. Polymorphisms in this gene are associated with susceptibility to myocardial infarction, coronary artery disease and cervical artery dissection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]
PHACTR1 Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy, 70Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- infantile spasmsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.566 AC: 86003AN: 151822Hom.: 26114 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
86003
AN:
151822
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.566 AC: 86037AN: 151940Hom.: 26121 Cov.: 32 AF XY: 0.576 AC XY: 42742AN XY: 74262 show subpopulations
GnomAD4 genome
AF:
AC:
86037
AN:
151940
Hom.:
Cov.:
32
AF XY:
AC XY:
42742
AN XY:
74262
show subpopulations
African (AFR)
AF:
AC:
14512
AN:
41394
American (AMR)
AF:
AC:
9135
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
2015
AN:
3468
East Asian (EAS)
AF:
AC:
4950
AN:
5162
South Asian (SAS)
AF:
AC:
3792
AN:
4818
European-Finnish (FIN)
AF:
AC:
7154
AN:
10554
Middle Eastern (MID)
AF:
AC:
145
AN:
290
European-Non Finnish (NFE)
AF:
AC:
42654
AN:
67972
Other (OTH)
AF:
AC:
1183
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1747
3494
5242
6989
8736
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
726
1452
2178
2904
3630
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2903
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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