rs12660697

Positions:

• chr6-8065474-G-A

Variant summary

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

The NR_037618.1(EEF1E1-BLOC1S5):​n.459-2858C>T 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 0.00357 in 152,332 control chromosomes in the GnomAD database, including 4 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 0.0036 (4 hom., cov: 33)
• Consequence: EEF1E1-BLOC1S5 NR_037618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

EEF1E1-BLOC1S5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00357 (544/152332) while in subpopulation EAS AF= 0.0374 (194/5188). AF 95% confidence interval is 0.0331. There are 4 homozygotes in gnomad4. There are 295 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEF1E1-BLOC1S5	NR_037618.1	n.459-2858C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00359 AC: 546 AN: 152214 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00347

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00235

Gnomad OTH AF: 0.00669

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

GnomAD4 genome AF: 0.00357 AC: 544 AN: 152332 Hom.: 4 Cov.: 33 AF XY: 0.00396 AC XY: 295 AN XY: 74496

Gnomad4 AFR AF: 0.000625

Gnomad4 AMR AF: 0.00346

Gnomad4 ASJ AF: 0.00779

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00235

Gnomad4 OTH AF: 0.00710

Alfa AF: 0.00287 Hom.: 2

Bravo AF: 0.00383

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.82

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: rs12660697; hg19: chr6-8065707;