chr11-31778325-G-C

Variant names:

• chr11-31778325-G-C
• rs7125966
• NM_019040.5:c.1144-5068G>C

Variant summary

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

The NM_019040.5(ELP4):​c.1144-5068G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,088 control chromosomes in the GnomAD database, including 37,832 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 0.70 (37832 hom., cov: 31)
• Consequence: ELP4 NM_019040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELP4	NM_019040.5	c.1144-5068G>C		intron_variant	Intron 9 of 9	ENST00000640961.2	NP_061913.3
ELP4	NM_001288726.2	c.1572-5068G>C		intron_variant	Intron 11 of 11		NP_001275655.1
ELP4	NM_001288725.2	c.1286-5068G>C		intron_variant	Intron 10 of 10		NP_001275654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELP4	ENST00000640961.2	c.1144-5068G>C		intron_variant	Intron 9 of 9	1	NM_019040.5	ENSP00000492152.1

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105733 AN: 151970 Hom.: 37771 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.696 AC: 105856 AN: 152088 Hom.: 37832 Cov.: 31 AF XY: 0.688 AC XY: 51170 AN XY: 74346

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.712

Alfa AF: 0.675 Hom.: 4422

Bravo AF: 0.704

Asia WGS AF: 0.582 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.54

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: rs7125966; hg19: chr11-31799873;