rs114665741
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000282041.11(EPG5):c.6516C>T(p.Tyr2172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,613,970 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0090 ( 14 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 25 hom. )
Consequence
EPG5
ENST00000282041.11 synonymous
ENST00000282041.11 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.824
Genes affected
EPG5 (HGNC:29331): (ectopic P-granules 5 autophagy tethering factor) This gene encodes a large coiled coil domain-containing protein that functions in autophagy during starvation conditions. Mutations in this gene cause Vici syndrome. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 18-45866903-G-A is Benign according to our data. Variant chr18-45866903-G-A is described in ClinVar as [Benign]. Clinvar id is 534617.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.824 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00897 (1366/152280) while in subpopulation AFR AF= 0.0254 (1054/41556). AF 95% confidence interval is 0.0241. There are 14 homozygotes in gnomad4. There are 654 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPG5 | NM_020964.3 | c.6516C>T | p.Tyr2172= | synonymous_variant | 38/44 | ENST00000282041.11 | NP_066015.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPG5 | ENST00000282041.11 | c.6516C>T | p.Tyr2172= | synonymous_variant | 38/44 | 1 | NM_020964.3 | ENSP00000282041 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00894 AC: 1361AN: 152162Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00400 AC: 997AN: 249512Hom.: 7 AF XY: 0.00348 AC XY: 471AN XY: 135368
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GnomAD4 exome AF: 0.00224 AC: 3276AN: 1461690Hom.: 25 Cov.: 32 AF XY: 0.00222 AC XY: 1616AN XY: 727180
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GnomAD4 genome AF: 0.00897 AC: 1366AN: 152280Hom.: 14 Cov.: 32 AF XY: 0.00878 AC XY: 654AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 23, 2020 | - - |
Vici syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at