chr8-28136724-T-G

Position:

• chr8-28136724-T-G

Variant summary

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

The NM_018091.6(ELP3):​c.907-974T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,100 control chromosomes in the GnomAD database, including 28,197 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 (28197 hom., cov: 32)
• Consequence: ELP3 NM_018091.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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]

ELP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP3	NM_018091.6	c.907-974T>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.907-974T>G		intron_variant		1	NM_018091.6	ENSP00000256398.8

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89204 AN: 151982 Hom.: 28138 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.587 AC: 89329 AN: 152100 Hom.: 28197 Cov.: 32 AF XY: 0.593 AC XY: 44104 AN XY: 74372

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.559

Alfa AF: 0.507 Hom.: 9652

Bravo AF: 0.609

Asia WGS AF: 0.744 AC: 2583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.27
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: rs4732828; hg19: chr8-27994241;