rs11031419

Variant names:

• chr11-31584349-A-T
• rs11031419
• NM_019040.5:c.382-10421A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• aniridia 2

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Genomics England PanelApp
• aniridia 1

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ELP4	NM_019040.5	c.382-10421A>T		intron_variant	Intron 3 of 9	ENST00000640961.2	NP_061913.3
ELP4	NM_001288726.2	c.382-10421A>T		intron_variant	Intron 3 of 11		NP_001275655.1
ELP4	NM_001288725.2	c.382-10421A>T		intron_variant	Intron 3 of 10		NP_001275654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.382-10421A>T		intron_variant	Intron 3 of 9	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

African (AFR) AF: 0.0345 AC: 1433 AN: 41540

American (AMR) AF: 0.0334 AC: 510 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3468

East Asian (EAS) AF: 0.179 AC: 927 AN: 5180

South Asian (SAS) AF: 0.0544 AC: 263 AN: 4832

European-Finnish (FIN) AF: 0.0626 AC: 658 AN: 10516

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0320 AC: 2175 AN: 67984

Other (OTH) AF: 0.0522 AC: 110 AN: 2106

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
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11031419; hg19: chr11-31605896;