chr8-131953798-CTT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015137.6(EFR3A):c.489-6_489-5del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 1,323,574 control chromosomes in the GnomAD database, including 222 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.039 ( 191 hom., cov: 30)
Exomes 𝑓: 0.020 ( 31 hom. )
Consequence
EFR3A
NM_015137.6 intron
NM_015137.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.536
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 -10 ACMG points.
BP6
?
Variant 8-131953798-CTT-C is Benign according to our data. Variant chr8-131953798-CTT-C is described in ClinVar as [Benign]. Clinvar id is 3059061.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3A | NM_015137.6 | c.489-6_489-5del | intron_variant | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.489-6_489-5del | intron_variant | 1 | NM_015137.6 | P3 | |||
EFR3A | ENST00000519656.1 | c.381-6_381-5del | intron_variant | 1 | A1 | ||||
EFR3A | ENST00000522709.5 | c.381-6_381-5del | intron_variant | 5 | |||||
EFR3A | ENST00000637848.1 | c.570-6_570-5del | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0391 AC: 5428AN: 138656Hom.: 192 Cov.: 30
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GnomAD3 exomes AF: 0.0422 AC: 2320AN: 55024Hom.: 5 AF XY: 0.0401 AC XY: 1167AN XY: 29072
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GnomAD4 exome AF: 0.0203 AC: 24045AN: 1184938Hom.: 31 AF XY: 0.0201 AC XY: 11675AN XY: 579962
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GnomAD4 genome ? AF: 0.0391 AC: 5420AN: 138636Hom.: 191 Cov.: 30 AF XY: 0.0390 AC XY: 2616AN XY: 67082
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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 | May 03, 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at