11-31552099-T-C

Position:

• chr11-31552099-T-C

Variant summary

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

The NM_019040.5(ELP4):​c.381+12316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,988 control chromosomes in the GnomAD database, including 13,013 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 0.37 (13013 hom., cov: 32)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.381+12316T>C		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288725.2	c.381+12316T>C		intron_variant			NP_001275654.1
ELP4	NM_001288726.2	c.381+12316T>C		intron_variant			NP_001275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.381+12316T>C		intron_variant		1	NM_019040.5	ENSP00000492152	P3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55971 AN: 151870 Hom.: 12960 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.369 AC: 56089 AN: 151988 Hom.: 13013 Cov.: 32 AF XY: 0.363 AC XY: 26984 AN XY: 74304

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.384

Alfa AF: 0.307 Hom.: 2427

Bravo AF: 0.401

Asia WGS AF: 0.389 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.72

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: rs2104246; hg19: chr11-31573646;