6-8064997-T-C

Position:

• chr6-8064997-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_037618.1(EEF1E1-BLOC1S5):​n.459-2381A>G variant causes a intron, non coding transcript 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 NR_037618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

EEF1E1-BLOC1S5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.517

Alfa AF: 0.491 Hom.: 25311

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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;