rs9392956

chr6-8065536-C-T

Variant summary

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

The NR_037618.1(EEF1E1-BLOC1S5):n.459-2920G>A 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 0.0636 in 152,292 control chromosomes in the GnomAD database, including 520 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 0.064 (520 hom., cov: 33)
• Consequence: EEF1E1-BLOC1S5 NR_037618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

Genes affected

EEF1E1-BLOC1S5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEF1E1-BLOC1S5	NR_037618.1	n.459-2920G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9679 AN: 152174 Hom.: 522 Cov.: 33

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0636 AC: 9685 AN: 152292 Hom.: 520 Cov.: 33 AF XY: 0.0668 AC XY: 4973 AN XY: 74476

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0541 Hom.: 42

Bravo AF: 0.0700

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.0
Dann	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs9392956; hg19: chr6-8065769;