rs11031423

Positions:

• chr11-31597020-A-G
• chr11-31597020-A-T

Variant summary

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

The NM_019040.5(ELP4):​c.513+2119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 152,228 control chromosomes in the GnomAD database, including 889 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 0.093 (889 hom., cov: 33)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.513+2119A>G		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288725.2	c.513+2119A>G		intron_variant			NP_001275654.1
ELP4	NM_001288726.2	c.513+2119A>G		intron_variant			NP_001275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.513+2119A>G		intron_variant		1	NM_019040.5	ENSP00000492152	P3

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14183 AN: 152110 Hom.: 877 Cov.: 33

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0933 AC: 14203 AN: 152228 Hom.: 889 Cov.: 33 AF XY: 0.0920 AC XY: 6851 AN XY: 74446

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0648 Hom.: 104

Bravo AF: 0.0936

Asia WGS AF: 0.203 AC: 701 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.64

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: rs11031423; hg19: chr11-31618567;