rs11854468

Positions:

• chr15-35158348-C-T

Variant summary

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

The XM_047433263.1(DPH6):​c.*36-13210G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,080 control chromosomes in the GnomAD database, including 1,392 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 0.12 (1392 hom., cov: 33)
• Consequence: DPH6 XM_047433263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

DPH6 (HGNC:30543): (diphthamine biosynthesis 6) Enables diphthine-ammonia ligase activity. Predicted to be involved in peptidyl-diphthamide biosynthetic process from peptidyl-histidine. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPH6	XM_047433263.1	c.*36-13210G>A		intron_variant			XP_047289219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259336	ENST00000559246.1	n.74+11277G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18436 AN: 151962 Hom.: 1389 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.121 AC: 18462 AN: 152080 Hom.: 1392 Cov.: 33 AF XY: 0.118 AC XY: 8779 AN XY: 74348

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.126

Alfa AF: 0.102 Hom.: 1143

Bravo AF: 0.125

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11854468; hg19: chr15-35450549;