rs9392956

Variant names:

• chr6-8065536-C-T
• rs9392956
• ENST00000397456.2:n.385-2920G>A

Variant summary

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

The ENST00000397456.2(EEF1E1-BLOC1S5):​n.385-2920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,292 control chromosomes in the GnomAD database, including 520 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (520 hom., cov: 33)
• Consequence: EEF1E1-BLOC1S5 ENST00000397456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 2 publications found

Genes affected

EEF1E1-BLOC1S5 (HGNC:49187): (EEF1E1-BLOC1S5 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring EEF1E1 (eukaryotic translation elongation factor 1 epsilon 1) and MUTED (muted homolog) genes on chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1E1-BLOC1S5	NR_037618.1	n.459-2920G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1E1-BLOC1S5	ENST00000397456.2	n.385-2920G>A		intron_variant	Intron 3 of 6	3		ENSP00000380597.2

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9679 AN: 152174 Hom.: 522 Cov.: 33

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.0684

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0636 AC: 9685 AN: 152292 Hom.: 520 Cov.: 33 AF XY: 0.0668 AC XY: 4973 AN XY: 74476

African (AFR) AF: 0.0306 AC: 1271 AN: 41560

American (AMR) AF: 0.142 AC: 2169 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1006 AN: 5184

South Asian (SAS) AF: 0.146 AC: 705 AN: 4824

European-Finnish (FIN) AF: 0.0372 AC: 395 AN: 10616

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0539 AC: 3664 AN: 68022

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0541 Hom.: 42

Bravo AF: 0.0700

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.55
PhyloP100		0.35

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: rs9392956; hg19: chr6-8065769;