rs10835793

Variant names:

• chr11-31597303-T-A
• rs10835793
• NM_019040.5:c.513+2402T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-31597303-T-A
• chr11-31597303-T-C
• chr11-31597303-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019040.5(ELP4):​c.513+2402T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,022 control chromosomes in the GnomAD database, including 33,398 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 0.64 (33398 hom., cov: 31)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 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
• ocular dysgenesis caused by defects in PAX6 regulation

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019040.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELP4	NM_019040.5	MANE Select	c.513+2402T>A		intron	N/A	NP_061913.3
	ELP4	NM_001288726.2		c.513+2402T>A		intron	N/A	NP_001275655.1	G5E9D4
	ELP4	NM_001288725.2		c.513+2402T>A		intron	N/A	NP_001275654.1	Q96EB1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELP4	ENST00000640961.2	TSL:1 MANE Select	c.513+2402T>A		intron	N/A	ENSP00000492152.1	Q96EB1-1
	ELP4	ENST00000395934.2	TSL:1	c.513+2402T>A		intron	N/A	ENSP00000379267.2	G5E9D4
	ELP4	ENST00000379163.10	TSL:2	c.513+2402T>A		intron	N/A	ENSP00000368461.5	Q96EB1-3

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97224 AN: 151904 Hom.: 33402 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.640 AC: 97228 AN: 152022 Hom.: 33398 Cov.: 31 AF XY: 0.645 AC XY: 47956 AN XY: 74298

African (AFR) AF: 0.375 AC: 15537 AN: 41442

American (AMR) AF: 0.617 AC: 9422 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3413 AN: 5130

South Asian (SAS) AF: 0.659 AC: 3176 AN: 4822

European-Finnish (FIN) AF: 0.884 AC: 9362 AN: 10588

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51685 AN: 67986

Other (OTH) AF: 0.624 AC: 1317 AN: 2112

Alfa AF: 0.689 Hom.: 4692

Bravo AF: 0.608

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		0.0020
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: rs10835793; hg19: chr11-31618850;