11-31631665-G-A

Position:

• chr11-31631665-G-A

Variant summary

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

The NM_019040.5(ELP4):​c.739-552G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,964 control chromosomes in the GnomAD database, including 12,114 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 0.36 (12114 hom., cov: 33)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELP4	NM_019040.5	c.739-552G>A		intron_variant		ENST00000640961.2
ELP4	NM_001288725.2	c.742-552G>A		intron_variant
ELP4	NM_001288726.2	c.739-552G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELP4	ENST00000640961.2	c.739-552G>A		intron_variant		1	NM_019040.5	P3
	ENST00000648611.1	n.845-216C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55364 AN: 151846 Hom.: 12118 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.364 AC: 55351 AN: 151964 Hom.: 12114 Cov.: 33 AF XY: 0.373 AC XY: 27708 AN XY: 74262

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.363

Alfa AF: 0.404 Hom.: 1760

Bravo AF: 0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.50

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: rs11031434; hg19: chr11-31653212;