rs10488688

chr11-31767566-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019040.5(ELP4):c.1144-15827G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,854 control chromosomes in the GnomAD database, including 4,503 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 0.23 (4503 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELP4	NM_019040.5	c.1144-15827G>C		intron_variant		ENST00000640961.2
ELP4	NM_001288725.2	c.1285+4017G>C		intron_variant
ELP4	NM_001288726.2	c.1571+4017G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELP4	ENST00000640961.2	c.1144-15827G>C		intron_variant		1	NM_019040.5	P3
	ENST00000648611.1	n.288+69C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34918 AN: 151738 Hom.: 4502 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.225

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.230 AC: 34918 AN: 151854 Hom.: 4503 Cov.: 32 AF XY: 0.228 AC XY: 16945 AN XY: 74232

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.221

Alfa AF: 0.253 Hom.: 634

Bravo AF: 0.221

Asia WGS AF: 0.107 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	13
Dann	Benign	0.60

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: rs10488688; hg19: chr11-31789114;