8-28184670-A-G

Position:

• chr8-28184670-A-G

Variant summary

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

The ENST00000256398.13(ELP3):​c.1568-4979A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,972 control chromosomes in the GnomAD database, including 20,806 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 0.52 (20806 hom., cov: 32)
• Consequence: ELP3 ENST00000256398.13 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

ELP3 (HGNC:20696): (elongator acetyltransferase complex subunit 3) Enables acetyltransferase activity and phosphorylase kinase regulator activity. Involved in regulation of transcription by RNA polymerase II and tRNA wobble uridine modification. Located in cytosol and nucleolus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP3	NM_018091.6	c.1568-4979A>G		intron_variant		ENST00000256398.13	NP_060561.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP3	ENST00000256398.13	c.1568-4979A>G		intron_variant		1	NM_018091.6	ENSP00000256398	P1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79071 AN: 151854 Hom.: 20800 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.521 AC: 79106 AN: 151972 Hom.: 20806 Cov.: 32 AF XY: 0.515 AC XY: 38245 AN XY: 74238

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.548

Alfa AF: 0.543 Hom.: 11176

Bravo AF: 0.522

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.75

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: rs4732838; hg19: chr8-28042187;