3-68977324-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001278689.2(EOGT):c.*293del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0049 (2 hom., cov: 31)
  • Exomes 𝑓: 0.21 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EOGT NM_001278689.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.603

Genes affected

EOGT (HGNC:28526): (EGF domain specific O-linked N-acetylglucosamine transferase) This gene encodes an enzyme that acts in the lumen of the endoplasmic reticulum to catalyze the transfer of N-acetylglucosamine to serine or threonine residues of extracellular-targeted proteins. This enzyme modifies proteins containing eukaryotic growth factor (EGF)-like domains, including the Notch receptor, thereby regulating developmental signalling. Mutations in this gene have been observed in individuals with Adams-Oliver syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-68977324-CA-C is Benign according to our data. Variant chr3-68977324-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1213680.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EOGT	NM_001278689.2	c.*293del		3_prime_UTR_variant	18/18	ENST00000383701.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EOGT	ENST00000383701.8	c.*293del		3_prime_UTR_variant	18/18	1	NM_001278689.2	P1
EOGT	ENST00000295571.9	c.*293del		3_prime_UTR_variant	15/15	1
EOGT	ENST00000496647.5	n.1531del		non_coding_transcript_exon_variant	9/9	2
EOGT	ENST00000403140.6	c.*1045del		3_prime_UTR_variant, NMD_transcript_variant	16/16	2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 583 AN: 119586 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.00735

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00337

Gnomad ASJ AF: 0.00252

Gnomad EAS AF: 0.000711

Gnomad SAS AF: 0.000269

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.00315

Gnomad OTH AF: 0.00447

GnomAD4 exome AF: 0.213 AC: 13066 AN: 61356 Hom.: 0 Cov.: 0 AF XY: 0.212 AC XY: 6954 AN XY: 32806

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00495 AC: 592 AN: 119630 Hom.: 2 Cov.: 31 AF XY: 0.00524 AC XY: 299 AN XY: 57098

Gnomad4 AFR AF: 0.00752

Gnomad4 AMR AF: 0.00345

Gnomad4 ASJ AF: 0.00252

Gnomad4 EAS AF: 0.000713

Gnomad4 SAS AF: 0.000271

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.00315

Gnomad4 OTH AF: 0.00506

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs59164738; hg19: chr3-69026475;