18-45865765-CAAAAAAA-CAAAAAAAAAAAAAAAAAA

Variant names:

• chr18-45865765-C-CAAAAAAAAAAA
• rs11333207
• NM_020964.3:c.6622-17_6622-7dupTTTTTTTTTTT

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BS1 BS2

The NM_020964.3(EPG5):​c.6622-17_6622-7dupTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000651 in 1,410,880 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0069 (4 hom., cov: 25)
  • Exomes 𝑓: 0.00016 (0 hom.)
• Consequence: EPG5 NM_020964.3 splice_region, intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.327

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]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 18-45865765-C-CAAAAAAAAAAA is Benign according to our data. Variant chr18-45865765-C-CAAAAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 1107893.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00692 (709/102384) while in subpopulation AFR AF= 0.0209 (525/25068). AF 95% confidence interval is 0.0195. There are 4 homozygotes in gnomad4. There are 340 alleles in male gnomad4 subpopulation. Median coverage is 25. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPG5	NM_020964.3	c.6622-17_6622-7dupTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 38 of 43	ENST00000282041.11	NP_066015.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPG5	ENST00000282041.11	c.6622-7_6622-6insTTTTTTTTTTT		splice_region_variant, intron_variant	Intron 38 of 43	1	NM_020964.3	ENSP00000282041.4

Frequencies

GnomAD3 genomes AF: 0.00691 AC: 707 AN: 102376 Hom.: 4 Cov.: 25

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.00169

Gnomad AMR AF: 0.00671

Gnomad ASJ AF: 0.00210

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000549

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00177

Gnomad OTH AF: 0.0105

GnomAD4 exome AF: 0.000160 AC: 210 AN: 1308496 Hom.: 0 Cov.: 0 AF XY: 0.000158 AC XY: 102 AN XY: 647134

Gnomad4 AFR exome AF: 0.00234

Gnomad4 AMR exome AF: 0.000423

Gnomad4 ASJ exome AF: 0.000339

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000734

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000915

Gnomad4 OTH exome AF: 0.000368

GnomAD4 genome AF: 0.00692 AC: 709 AN: 102384 Hom.: 4 Cov.: 25 AF XY: 0.00691 AC XY: 340 AN XY: 49188

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.00670

Gnomad4 ASJ AF: 0.00210

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000551

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00177

Gnomad4 OTH AF: 0.0104

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

EPG5-related disorder Benign:1

May 15, 2024

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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). -

not provided Benign:1

Sep 01, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Vici syndrome Benign:1

Dec 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11333207; hg19: chr18-43445730;