11-31726210-T-C

Position:

• chr11-31726210-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.1144-57183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,920 control chromosomes in the GnomAD database, including 7,518 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 0.30 (7518 hom., cov: 31)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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]

ENSG00000228061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.1144-57183T>C		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288726.2	c.1433-37201T>C		intron_variant			NP_001275655.1
ELP4	NM_001288725.2	c.1147-37201T>C		intron_variant			NP_001275654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.1144-57183T>C		intron_variant		1	NM_019040.5	ENSP00000492152.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45751 AN: 151804 Hom.: 7496 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.302 AC: 45807 AN: 151920 Hom.: 7518 Cov.: 31 AF XY: 0.297 AC XY: 22068 AN XY: 74280

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.331

Alfa AF: 0.279 Hom.: 801

Bravo AF: 0.314

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.78

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: rs12365798; hg19: chr11-31747758;