11-31700936-C-T

Position:

• chr11-31700936-C-T

Variant summary

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

The NM_019040.5(ELP4):​c.1143+50715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,856 control chromosomes in the GnomAD database, including 8,637 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 (8637 hom., cov: 31)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELP4	NM_019040.5	c.1143+50715C>T		intron_variant		ENST00000640961.2
ELP4	NM_001288725.2	c.1146+50715C>T		intron_variant
ELP4	NM_001288726.2	c.1432+18861C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELP4	ENST00000640961.2	c.1143+50715C>T		intron_variant		1	NM_019040.5	P3
	ENST00000648611.1	n.549+26851G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46246 AN: 151738 Hom.: 8640 Cov.: 31

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.304 AC: 46238 AN: 151856 Hom.: 8637 Cov.: 31 AF XY: 0.310 AC XY: 23020 AN XY: 74174

Gnomad4 AFR AF: 0.0771

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.292

Alfa AF: 0.377 Hom.: 10212

Bravo AF: 0.281

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.68

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: rs10835810; hg19: chr11-31722484;