rs4557499

chr6-63480642-G-T

Variant summary

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

The ENST00000444820.2(EEF1B2P5):n.447+62G>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 0.465 in 151,716 control chromosomes in the GnomAD database, including 18,203 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 0.46 (18188 hom., cov: 30)
  • Exomes 𝑓: 0.67 (15 hom.)
• Consequence: EEF1B2P5 ENST00000444820.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

EEF1B2P5 (HGNC:32476): (eukaryotic translation elongation factor 1 beta 2 pseudogene 5)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGSN	XM_047418866.1	c.-963-36884C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEF1B2P5	ENST00000444820.2	n.447+62G>T		intron_variant, non_coding_transcript_variant
	ENST00000701584.1	n.134-36884C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70479 AN: 151528 Hom.: 18197 Cov.: 30

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.507

GnomAD4 exome AF: 0.671 AC: 47 AN: 70 Hom.: 15 AF XY: 0.667 AC XY: 32 AN XY: 48

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.729

Gnomad4 NFE exome AF: 0.643

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.465 AC: 70474 AN: 151646 Hom.: 18188 Cov.: 30 AF XY: 0.469 AC XY: 34722 AN XY: 74094

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.506

Alfa AF: 0.500 Hom.: 2978

Bravo AF: 0.443

Asia WGS AF: 0.547 AC: 1903 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.4
Dann	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4557499; hg19: chr6-64190547;