rs114665741

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.824
Variant links:
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]

Genome browser will be placed here

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
EPG5NM_020964.3 linkuse as main transcriptc.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
EPG5ENST00000282041.11 linkuse as main transcriptc.6516C>T p.Tyr2172= synonymous_variant 38/441 NM_020964.3 ENSP00000282041 P4Q9HCE0-1

Frequencies

GnomAD3 genomes
AF:
0.00894
AC:
1361
AN:
152162
Hom.:
14
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0253
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0104
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000829
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.00166
Gnomad OTH
AF:
0.0105
GnomAD3 exomes
AF:
0.00400
AC:
997
AN:
249512
Hom.:
7
AF XY:
0.00348
AC XY:
471
AN XY:
135368
show subpopulations
Gnomad AFR exome
AF:
0.0287
Gnomad AMR exome
AF:
0.00698
Gnomad ASJ exome
AF:
0.00238
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000719
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00202
Gnomad OTH exome
AF:
0.00594
GnomAD4 exome
AF:
0.00224
AC:
3276
AN:
1461690
Hom.:
25
Cov.:
32
AF XY:
0.00222
AC XY:
1616
AN XY:
727180
show subpopulations
Gnomad4 AFR exome
AF:
0.0267
Gnomad4 AMR exome
AF:
0.00693
Gnomad4 ASJ exome
AF:
0.00253
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000742
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.00134
Gnomad4 OTH exome
AF:
0.00537
GnomAD4 genome
AF:
0.00897
AC:
1366
AN:
152280
Hom.:
14
Cov.:
32
AF XY:
0.00878
AC XY:
654
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0254
Gnomad4 AMR
AF:
0.0104
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00165
Gnomad4 OTH
AF:
0.0104
Alfa
AF:
0.00505
Hom.:
1
Bravo
AF:
0.0110
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.00273
EpiControl
AF:
0.00261

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 23, 2020- -
Vici syndrome Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
2.3
DANN
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs114665741; hg19: chr18-43446868; API