chr4-145112254-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_002940.3(ABCE1):c.726G>A(p.Glu242=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,435,060 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 11 hom., cov: 31)
Exomes 𝑓: 0.00057 ( 13 hom. )
Consequence
ABCE1
NM_002940.3 synonymous
NM_002940.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.18
Genes affected
ABCE1 (HGNC:69): (ATP binding cassette subfamily E member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the OABP subfamily. Alternatively referred to as the RNase L inhibitor, this protein functions to block the activity of ribonuclease L. Activation of ribonuclease L leads to inhibition of protein synthesis in the 2-5A/RNase L system, the central pathway for viral interferon action. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
OTUD4 (HGNC:24949): (OTU deubiquitinase 4) Alternatively spliced transcript variants have been found for this gene. The smaller protein isoform encoded by the shorter transcript variant is found only in HIV-1 infected cells. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 4-145112254-G-A is Benign according to our data. Variant chr4-145112254-G-A is described in ClinVar as [Benign]. Clinvar id is 714248.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.18 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0062 (901/145406) while in subpopulation AFR AF= 0.0223 (875/39238). AF 95% confidence interval is 0.0211. There are 11 homozygotes in gnomad4. There are 436 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 900 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCE1 | NM_002940.3 | c.726G>A | p.Glu242= | synonymous_variant | 9/18 | ENST00000296577.9 | |
ABCE1 | NM_001040876.2 | c.726G>A | p.Glu242= | synonymous_variant | 9/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCE1 | ENST00000296577.9 | c.726G>A | p.Glu242= | synonymous_variant | 9/18 | 1 | NM_002940.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00619 AC: 900AN: 145318Hom.: 11 Cov.: 31
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GnomAD3 exomes AF: 0.00139 AC: 292AN: 209926Hom.: 4 AF XY: 0.00118 AC XY: 134AN XY: 114024
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GnomAD4 exome AF: 0.000571 AC: 737AN: 1289654Hom.: 13 Cov.: 30 AF XY: 0.000523 AC XY: 337AN XY: 644746
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at