6-8064997-T-C

Variant names:

• chr6-8064997-T-C
• rs2815155
• ENST00000397456.2:n.385-2381A>G

Variant summary

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

The ENST00000397456.2(EEF1E1-BLOC1S5):​n.385-2381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,102 control chromosomes in the GnomAD database, including 27,337 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 0.59 (27337 hom., cov: 32)
• Consequence: EEF1E1-BLOC1S5 ENST00000397456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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.459-2381A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1E1-BLOC1S5	ENST00000397456.2	TSL:3	n.385-2381A>G		intron	N/A	ENSP00000380597.2	C9J1V9

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88976 AN: 151984 Hom.: 27296 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.586 AC: 89080 AN: 152102 Hom.: 27337 Cov.: 32 AF XY: 0.588 AC XY: 43715 AN XY: 74346

African (AFR) AF: 0.762 AC: 31597 AN: 41488

American (AMR) AF: 0.539 AC: 8233 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4177 AN: 5176

South Asian (SAS) AF: 0.672 AC: 3239 AN: 4820

European-Finnish (FIN) AF: 0.527 AC: 5566 AN: 10568

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33159 AN: 67976

Other (OTH) AF: 0.517 AC: 1091 AN: 2110

Alfa AF: 0.502 Hom.: 37151

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.83
PhyloP100		0.074

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: rs2815155;

hg19: chr6-8065230;