rs2863231

Positions:

• chr11-31775012-A-G

Variant summary

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

The NM_019040.5(ELP4):​c.1144-8381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,026 control chromosomes in the GnomAD database, including 39,240 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 0.71 (39240 hom., cov: 31)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

ELP4 (HGNC:1171): (elongator acetyltransferase complex subunit 4) This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of yeast ELP4 deletion mutants. This gene has also been associated with Rolandic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ELP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.1144-8381A>G		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288726.2	c.1572-8381A>G		intron_variant			NP_001275655.1
ELP4	NM_001288725.2	c.1286-8381A>G		intron_variant			NP_001275654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.1144-8381A>G		intron_variant		1	NM_019040.5	ENSP00000492152.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107285 AN: 151908 Hom.: 39171 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.707 AC: 107415 AN: 152026 Hom.: 39240 Cov.: 31 AF XY: 0.698 AC XY: 51875 AN XY: 74318

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.726

Alfa AF: 0.668 Hom.: 34534

Bravo AF: 0.716

Asia WGS AF: 0.590 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.77

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: rs2863231; hg19: chr11-31796560;