chr6-8066053-T-G

Variant names:

• chr6-8066053-T-G
• rs9505351
• ENST00000397456.2:n.385-3437A>C

Variant summary

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

The ENST00000397456.2(EEF1E1-BLOC1S5):​n.385-3437A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,054 control chromosomes in the GnomAD database, including 6,389 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 0.28 (6389 hom., cov: 32)
• Consequence: EEF1E1-BLOC1S5 ENST00000397456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1E1-BLOC1S5	NR_037618.1	n.459-3437A>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1E1-BLOC1S5	ENST00000397456.2	n.385-3437A>C		intron_variant	Intron 3 of 6	3		ENSP00000380597.2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42682 AN: 151936 Hom.: 6379 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.281 AC: 42730 AN: 152054 Hom.: 6389 Cov.: 32 AF XY: 0.286 AC XY: 21249 AN XY: 74318

African (AFR) AF: 0.280 AC: 11628 AN: 41476

American (AMR) AF: 0.262 AC: 4011 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2916 AN: 5170

South Asian (SAS) AF: 0.236 AC: 1133 AN: 4810

European-Finnish (FIN) AF: 0.369 AC: 3894 AN: 10556

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17772 AN: 67974

Other (OTH) AF: 0.233 AC: 493 AN: 2112

Alfa AF: 0.268 Hom.: 16955

Bravo AF: 0.275

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.81
PhyloP100		-0.55

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: rs9505351; hg19: chr6-8066286;