19-10115376-G-A

Variant names:

• chr19-10115376-G-A
• rs2305795
• NM_003755.5:c.947+103C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003755.5(EIF3G):​c.947+103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 1,335,272 control chromosomes in the GnomAD database, including 221,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.60 (27386 hom., cov: 33)
  • Exomes 𝑓: 0.57 (193714 hom.)
• Consequence: EIF3G NM_003755.5 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.20
• Publications: 41 publications found

Genes affected

EIF3G (HGNC:3274): (eukaryotic translation initiation factor 3 subunit G) This gene encodes a core subunit of the eukaryotic translation initiation factor 3 (eIF3) complex, which is required for initiation of protein translation. An N-terminal caspase cleavage product of the encoded protein may stimulate degradation of DNA. A mutation in this gene is associated with narcolepsy. [provided by RefSeq, Jul 2016]

P2RY11 (HGNC:8540): (purinergic receptor P2Y11) The product of this gene belongs to the family of G-protein coupled receptors. This family has several receptor subtypes with different pharmacological selectivity, which overlaps in some cases, for various adenosine and uridine nucleotides. This receptor is coupled to the stimulation of the phosphoinositide and adenylyl cyclase pathways and behaves as a selective purinoceptor. Naturally occuring read-through transcripts, resulting from intergenic splicing between this gene and an immediately upstream gene (PPAN, encoding peter pan homolog), have been found. The PPAN-P2RY11 read-through mRNA is ubiquitously expressed and encodes a fusion protein that shares identity with each individual gene product. [provided by RefSeq, Jul 2008]

PPAN-P2RY11 (HGNC:33526): (PPAN-P2RY11 readthrough) This locus represents naturally occurring read-through transcription between the adjacent PPAN and P2RY11 genes. Alternative splicing results in two transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. This transcript is found to be ubiquitously expressed and is up-regulated by agents inducing granulocytic differentiation. However, its functional significance in vivo remains unclear. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003755.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF3G	NM_003755.5	MANE Select	c.947+103C>T		intron	N/A	NP_003746.2
	P2RY11	NM_002566.5	MANE Select	c.*638G>A		downstream_gene	N/A	NP_002557.2
	PPAN-P2RY11	NM_001040664.3		c.*638G>A		downstream_gene	N/A	NP_001035754.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF3G	ENST00000253108.9	TSL:1 MANE Select	c.947+103C>T		intron	N/A	ENSP00000253108.3
	EIF3G	ENST00000593054.5	TSL:5	c.341+103C>T		intron	N/A	ENSP00000467187.1
	EIF3G	ENST00000590158.1	TSL:2	n.966+103C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90619 AN: 151946 Hom.: 27341 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.619

GnomAD4 exome AF: 0.570 AC: 674411 AN: 1183208 Hom.: 193714 Cov.: 17 AF XY: 0.572 AC XY: 335184 AN XY: 585908

African (AFR) AF: 0.613 AC: 16441 AN: 26822

American (AMR) AF: 0.697 AC: 20217 AN: 29012

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 10424 AN: 18898

East Asian (EAS) AF: 0.683 AC: 25606 AN: 37498

South Asian (SAS) AF: 0.632 AC: 42332 AN: 67000

European-Finnish (FIN) AF: 0.594 AC: 29155 AN: 49062

Middle Eastern (MID) AF: 0.507 AC: 2434 AN: 4800

European-Non Finnish (NFE) AF: 0.554 AC: 498708 AN: 899992

Other (OTH) AF: 0.580 AC: 29094 AN: 50124

GnomAD4 genome AF: 0.597 AC: 90730 AN: 152064 Hom.: 27386 Cov.: 33 AF XY: 0.601 AC XY: 44666 AN XY: 74308

African (AFR) AF: 0.622 AC: 25796 AN: 41478

American (AMR) AF: 0.653 AC: 9974 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1939 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3600 AN: 5170

South Asian (SAS) AF: 0.642 AC: 3094 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6387 AN: 10582

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 38006 AN: 67958

Other (OTH) AF: 0.621 AC: 1310 AN: 2110

Alfa AF: 0.571 Hom.: 93646

Bravo AF: 0.604

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Cataplexy and narcolepsy Other:1

Dec 10, 2014

Center for Narcolepsy, Stanford University

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.31
DANN	Benign	0.41
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2305795; hg19: chr19-10226052;