chr8-131946572-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015137.6(EFR3A):āc.305A>Gā(p.His102Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0028 in 1,607,218 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0017 ( 10 hom., cov: 32)
Exomes š: 0.0029 ( 143 hom. )
Consequence
EFR3A
NM_015137.6 missense
NM_015137.6 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 5.32
Genes affected
EFR3A (HGNC:28970): (EFR3 homolog A) The protein encoded by this gene is part of a complex that plays a role in maintaining an active pool of phosphatidylinositol 4-kinase (PI4K) at the plasma membrane. This protein is thought to be a peripheral membrane protein that associates with the plasma membrane through palmitoylation. Studies indicate that this gene product plays a role in controlling G protein-coupled receptor (GPCR) activity by affecting receptor phosphorylation. Whole exome sequencing studies have implicated mutations in this gene with autism spectrum disorders. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.003976196).
BP6
Variant 8-131946572-A-G is Benign according to our data. Variant chr8-131946572-A-G is described in ClinVar as [Benign]. Clinvar id is 3046203.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00171 (261/152228) while in subpopulation SAS AF= 0.0526 (254/4826). AF 95% confidence interval is 0.0473. There are 10 homozygotes in gnomad4. There are 192 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3A | NM_015137.6 | c.305A>G | p.His102Arg | missense_variant | 4/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.305A>G | p.His102Arg | missense_variant | 4/23 | 1 | NM_015137.6 | P3 | |
EFR3A | ENST00000519656.1 | c.197A>G | p.His66Arg | missense_variant | 4/23 | 1 | A1 | ||
EFR3A | ENST00000637848.1 | c.386A>G | p.His129Arg | missense_variant | 4/23 | 5 | |||
EFR3A | ENST00000522709.5 | c.197A>G | p.His66Arg | missense_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 264AN: 152110Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00601 AC: 1455AN: 242292Hom.: 43 AF XY: 0.00825 AC XY: 1080AN XY: 130876
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GnomAD4 exome AF: 0.00291 AC: 4236AN: 1454990Hom.: 143 Cov.: 30 AF XY: 0.00417 AC XY: 3015AN XY: 723396
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GnomAD4 genome AF: 0.00171 AC: 261AN: 152228Hom.: 10 Cov.: 32 AF XY: 0.00258 AC XY: 192AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EFR3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;.;N
REVEL
Benign
Sift
Benign
T;T;.;T
Sift4G
Benign
T;T;.;T
Polyphen
B;.;.;.
Vest4
MVP
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at