chr6-8065548-C-A

Variant names:

• chr6-8065548-C-A
• rs9392957
• ENST00000397456.2:n.385-2932G>T

Variant summary

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

The ENST00000397456.2(EEF1E1-BLOC1S5):​n.385-2932G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,322 control chromosomes in the GnomAD database, including 747 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 0.086 (747 hom., cov: 33)
• Consequence: EEF1E1-BLOC1S5 ENST00000397456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397456.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1E1-BLOC1S5	NR_037618.1		n.459-2932G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1E1-BLOC1S5	ENST00000397456.2	TSL:3	n.385-2932G>T		intron	N/A	ENSP00000380597.2	C9J1V9

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13114 AN: 152204 Hom.: 750 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0861 AC: 13120 AN: 152322 Hom.: 747 Cov.: 33 AF XY: 0.0887 AC XY: 6610 AN XY: 74502

African (AFR) AF: 0.107 AC: 4463 AN: 41560

American (AMR) AF: 0.153 AC: 2334 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0913 AC: 317 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1008 AN: 5192

South Asian (SAS) AF: 0.145 AC: 699 AN: 4828

European-Finnish (FIN) AF: 0.0372 AC: 395 AN: 10624

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3694 AN: 68028

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0694 Hom.: 71

Bravo AF: 0.0957

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		-0.38

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9392957;

hg19: chr6-8065781;