11-31680968-G-T

Position:

• chr11-31680968-G-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+30747G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,972 control chromosomes in the GnomAD database, including 4,530 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 0.22 (4530 hom., cov: 32)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.1143+30747G>T		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288725.2	c.1146+30747G>T		intron_variant			NP_001275654.1
ELP4	NM_001288726.2	c.1144-819G>T		intron_variant			NP_001275655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.1143+30747G>T		intron_variant		1	NM_019040.5	ENSP00000492152	P3
	ENST00000648611.1	n.550-35212C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33161 AN: 151852 Hom.: 4531 Cov.: 32

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.218 AC: 33152 AN: 151972 Hom.: 4530 Cov.: 32 AF XY: 0.217 AC XY: 16093 AN XY: 74268

Gnomad4 AFR AF: 0.0650

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.214

Alfa AF: 0.247 Hom.: 2082

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.023
DANN	Benign	0.22

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: rs10488689; hg19: chr11-31702516;