rs10767903

chr11-31681804-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000395934.2(ELP4):c.1161C>T(p.His387=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 186,394 control chromosomes in the GnomAD database, including 41,836 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 0.61 (31420 hom., cov: 25)
  • Exomes 𝑓: 0.74 (10416 hom.)
• Consequence: ELP4 ENST00000395934.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BP7: Synonymous conserved (PhyloP=-0.969 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELP4	NM_019040.5	c.1143+31583C>T		intron_variant		ENST00000640961.2
ELP4	NM_001288726.2	c.1161C>T	p.His387=	synonymous_variant	10/12
ELP4	NM_001288725.2	c.1146+31583C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELP4	ENST00000640961.2	c.1143+31583C>T		intron_variant		1	NM_019040.5	P3
	ENST00000648611.1	n.550-36048G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.609 AC: 91168 AN: 149728 Hom.: 31428 Cov.: 25

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.610

GnomAD3 exomes AF: 0.663 AC: 988 AN: 1490 Hom.: 361 AF XY: 0.671 AC XY: 570 AN XY: 850

Gnomad AFR exome AF: 0.183

Gnomad AMR exome AF: 0.641

Gnomad ASJ exome AF: 0.776

Gnomad EAS exome AF: 0.736

Gnomad SAS exome AF: 0.694

Gnomad FIN exome AF: 0.875

Gnomad NFE exome AF: 0.740

Gnomad OTH exome AF: 0.565

GnomAD4 exome AF: 0.742 AC: 27119 AN: 36560 Hom.: 10416 Cov.: 0 AF XY: 0.730 AC XY: 15345 AN XY: 21010

Gnomad4 AFR exome AF: 0.270

Gnomad4 AMR exome AF: 0.629

Gnomad4 ASJ exome AF: 0.687

Gnomad4 EAS exome AF: 0.677

Gnomad4 SAS exome AF: 0.670

Gnomad4 FIN exome AF: 0.873

Gnomad4 NFE exome AF: 0.772

Gnomad4 OTH exome AF: 0.733

GnomAD4 genome AF: 0.608 AC: 91160 AN: 149834 Hom.: 31420 Cov.: 25 AF XY: 0.614 AC XY: 44865 AN XY: 73030

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.601

Alfa AF: 0.669 Hom.: 4572

Bravo AF: 0.571

Asia WGS AF: 0.602 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.38
Dann	Benign	0.69

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: rs10767903; hg19: chr11-31703352; COSMIC: COSV63349281;