rs11031419

Positions:

• chr11-31584349-A-T

Variant summary

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

The NM_019040.5(ELP4):​c.382-10421A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0412 in 152,114 control chromosomes in the GnomAD database, including 195 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 0.041 (195 hom., cov: 32)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

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]

ELP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP4	NM_019040.5	c.382-10421A>T		intron_variant		ENST00000640961.2	NP_061913.3
ELP4	NM_001288726.2	c.382-10421A>T		intron_variant			NP_001275655.1
ELP4	NM_001288725.2	c.382-10421A>T		intron_variant			NP_001275654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.382-10421A>T		intron_variant		1	NM_019040.5	ENSP00000492152.1

Frequencies

GnomAD3 genomes AF: 0.0412 AC: 6268 AN: 151998 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0412 AC: 6265 AN: 152114 Hom.: 195 Cov.: 32 AF XY: 0.0436 AC XY: 3245 AN XY: 74374

Gnomad4 AFR AF: 0.0345

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0544

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0315 Hom.: 9

Bravo AF: 0.0406

Asia WGS AF: 0.133 AC: 459 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.39

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: rs11031419; hg19: chr11-31605896;