chr11-31597303-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00200
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ELP4NM_019040.5 linkuse as main transcriptc.513+2402T>A intron_variant ENST00000640961.2
ELP4NM_001288725.2 linkuse as main transcriptc.513+2402T>A intron_variant
ELP4NM_001288726.2 linkuse as main transcriptc.513+2402T>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ELP4ENST00000640961.2 linkuse as main transcriptc.513+2402T>A intron_variant 1 NM_019040.5 P3Q96EB1-1

Frequencies

GnomAD3 genomes
AF:
0.640
AC:
97224
AN:
151904
Hom.:
33402
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.375
Gnomad4 AMR
AF:
0.617
Gnomad4 ASJ
AF:
0.690
Gnomad4 EAS
AF:
0.665
Gnomad4 SAS
AF:
0.659
Gnomad4 FIN
AF:
0.884
Gnomad4 NFE
AF:
0.760
Gnomad4 OTH
AF:
0.624
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
2.5
DANN
Benign
0.61

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10835793; hg19: chr11-31618850; API