rs2815155

Positions:

• chr6-8064997-T-A
• chr6-8064997-T-C
• chr6-8064997-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000397456.2(EEF1E1-BLOC1S5):​n.385-2381A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00336 in 152,156 control chromosomes in the GnomAD database, including 3 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 0.0034 (3 hom., cov: 32)
• Consequence: EEF1E1-BLOC1S5 ENST00000397456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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]

EEF1E1-BLOC1S5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00336 (511/152156) while in subpopulation EAS AF= 0.0303 (157/5178). AF 95% confidence interval is 0.0265. There are 3 homozygotes in gnomad4. There are 277 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEF1E1-BLOC1S5	NR_037618.1	n.459-2381A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1E1-BLOC1S5	ENST00000397456.2	n.385-2381A>T		intron_variant		3		ENSP00000380597.2

Frequencies

GnomAD3 genomes AF: 0.00337 AC: 512 AN: 152038 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000628

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00347

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.0000946

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00241

Gnomad OTH AF: 0.00670

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

GnomAD4 genome AF: 0.00336 AC: 511 AN: 152156 Hom.: 3 Cov.: 32 AF XY: 0.00372 AC XY: 277 AN XY: 74386

Gnomad4 AFR AF: 0.000626

Gnomad4 AMR AF: 0.00346

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0000946

Gnomad4 NFE AF: 0.00241

Gnomad4 OTH AF: 0.00711

Alfa AF: 0.0000147 Hom.: 25311

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.74

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: rs2815155; hg19: chr6-8065230;