NM_181706.5:c.111+12078G>A

Variant names:

• chr11-31382937-G-A
• rs578666
• NM_181706.5:c.111+12078G>A

Variant summary

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

The NM_181706.5(DNAJC24):​c.111+12078G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,012 control chromosomes in the GnomAD database, including 39,452 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 0.71 (39452 hom., cov: 32)
• Consequence: DNAJC24 NM_181706.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 7 publications found

Genes affected

DNAJC24 (HGNC:26979): (DnaJ heat shock protein family (Hsp40) member C24) Diphthamide is a unique posttranslationally modified histidine found only in translation elongation factor-2 (EEF2; MIM 130610). This modification is conserved from archaebacteria to humans and serves as the target for ADP-ribosylation and inactivation of EEF2 by diphtheria toxin (DT) and Pseudomonas exotoxin A. DPH4 is 1 of several enzymes involved in synthesis of diphthamide in EEF2 (Liu et al., 2004 [PubMed 15485916]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181706.5. 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
	DNAJC24	NM_181706.5	MANE Select	c.111+12078G>A		intron	N/A	NP_859057.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC24	ENST00000465995.6	TSL:1 MANE Select	c.111+12078G>A		intron	N/A	ENSP00000417548.1	Q6P3W2-1
	DNAJC24	ENST00000526042.5	TSL:1	n.111+12078G>A		intron	N/A	ENSP00000435771.1	Q6P3W2-2
	DNAJC24	ENST00000910453.1		c.111+12078G>A		intron	N/A	ENSP00000580512.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107370 AN: 151894 Hom.: 39389 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.707 AC: 107498 AN: 152012 Hom.: 39452 Cov.: 32 AF XY: 0.698 AC XY: 51866 AN XY: 74294

African (AFR) AF: 0.901 AC: 37404 AN: 41496

American (AMR) AF: 0.717 AC: 10944 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1902 AN: 5168

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4818

European-Finnish (FIN) AF: 0.531 AC: 5582 AN: 10512

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43720 AN: 67962

Other (OTH) AF: 0.723 AC: 1526 AN: 2110

Alfa AF: 0.655 Hom.: 43998

Bravo AF: 0.730

Asia WGS AF: 0.545 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.35
PhyloP100		0.036
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: rs578666; hg19: chr11-31404484;