ENST00000560832.1:n.26+11364T>C

Variant names:

• chr15-35193188-T-C
• rs12900262
• ENST00000560832.1:n.26+11364T>C

Variant summary

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

The ENST00000560832.1(ENSG00000293367):​n.26+11364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,962 control chromosomes in the GnomAD database, including 23,270 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 0.50 (23270 hom., cov: 32)
• Consequence: ENSG00000293367 ENST00000560832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 2 publications found

Genes affected

ENSG00000293367 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH6	XM_047433263.1	c.*36-48050A>G		intron_variant	Intron 9 of 9		XP_047289219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293367	ENST00000560832.1	n.26+11364T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75279 AN: 151844 Hom.: 23272 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.495 AC: 75269 AN: 151962 Hom.: 23270 Cov.: 32 AF XY: 0.496 AC XY: 36851 AN XY: 74252

African (AFR) AF: 0.126 AC: 5217 AN: 41524

American (AMR) AF: 0.491 AC: 7489 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2029 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1655 AN: 5180

South Asian (SAS) AF: 0.558 AC: 2688 AN: 4816

European-Finnish (FIN) AF: 0.697 AC: 7344 AN: 10532

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.690 AC: 46873 AN: 67884

Other (OTH) AF: 0.536 AC: 1132 AN: 2112

Alfa AF: 0.620 Hom.: 12356

Bravo AF: 0.461

Asia WGS AF: 0.440 AC: 1522 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.49
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12900262; hg19: chr15-35485389;