chr8-131953872-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_015137.6(EFR3A):c.543C>T(p.Asn181=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000409 in 1,572,810 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00020 ( 4 hom. )
Consequence
EFR3A
NM_015137.6 synonymous
NM_015137.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.432
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 Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 8-131953872-C-T is Benign according to our data. Variant chr8-131953872-C-T is described in ClinVar as [Benign]. Clinvar id is 3058019.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.432 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3A | NM_015137.6 | c.543C>T | p.Asn181= | synonymous_variant | 6/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.543C>T | p.Asn181= | synonymous_variant | 6/23 | 1 | NM_015137.6 | P3 | |
EFR3A | ENST00000519656.1 | c.435C>T | p.Asn145= | synonymous_variant | 6/23 | 1 | A1 | ||
EFR3A | ENST00000637848.1 | c.624C>T | p.Asn208= | synonymous_variant | 6/23 | 5 | |||
EFR3A | ENST00000522709.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00239 AC: 359AN: 150160Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000671 AC: 133AN: 198144Hom.: 0 AF XY: 0.000447 AC XY: 47AN XY: 105032
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GnomAD4 exome AF: 0.000200 AC: 284AN: 1422554Hom.: 4 Cov.: 33 AF XY: 0.000155 AC XY: 109AN XY: 704024
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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 | Aug 24, 2021 | 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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BayesDel_noAF
Benign
Cadd
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at