rs141093779

Variant names:

• chr15-44550909-G-A
• rs141093779
• NM_003758.4:c.181G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-44550909-G-A
• chr15-44550909-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003758.4(EIF3J):​c.181G>A​(p.Glu61Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EIF3J NM_003758.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83

Genes affected

EIF3J (HGNC:3270): (eukaryotic translation initiation factor 3 subunit J) This gene encodes a core subunit of the eukaryotic initiation factor 3 complex, which participates in the initiation of translation by aiding in the recruitment of protein and mRNA components to the 40S ribosome. There are pseudogenes for this gene on chromosomes 1, 3, and 9. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14154762).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF3J	NM_003758.4	c.181G>A	p.Glu61Lys	missense_variant	Exon 3 of 8	ENST00000261868.10	NP_003749.2
EIF3J	NM_001284335.2	c.181G>A	p.Glu61Lys	missense_variant	Exon 3 of 7		NP_001271264.1
EIF3J	NM_001284336.2	c.148-3644G>A		intron_variant	Intron 2 of 5		NP_001271265.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF3J	ENST00000261868.10	c.181G>A	p.Glu61Lys	missense_variant	Exon 3 of 8	1	NM_003758.4	ENSP00000261868.5
EIF3J	ENST00000535391.5	c.181G>A	p.Glu61Lys	missense_variant	Exon 3 of 7	2		ENSP00000440221.1
EIF3J	ENST00000424492.7	c.148-3644G>A		intron_variant	Intron 2 of 5	4		ENSP00000414548.3
EIF3J	ENST00000558227.1	n.227G>A		non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.019	T;.
Eigen	Benign	-0.23
Eigen_PC	Benign	0.012
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.70	T;T
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.050	N;N
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-1.5	N;N
REVEL	Benign	0.057
Sift	Benign	0.40	T;T
Sift4G	Benign	0.24	T;T
Polyphen		0.13	B;.
Vest4		0.48
MutPred		0.44		Gain of methylation at E61 (P = 0.0169);Gain of methylation at E61 (P = 0.0169);
MVP		0.26
MPC		0.37
ClinPred		0.76	D
GERP RS		5.6
Varity_R		0.19
gMVP		0.043

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: rs141093779; hg19: chr15-44843107;