1-43970973-G-T

Variant names:

• chr1-43970973-G-T
• rs760762295
• NM_001384.5:c.268G>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001319171.2(DPH2):​c.-208G>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000317 in 1,576,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00019 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: DPH2 NM_001319171.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.75
• Publications: 0 publications found

Genes affected

DPH2 (HGNC:3004): (diphthamide biosynthesis 2) This gene is one of two human genes similar to the yeast gene dph2. The yeast gene was identified by its ability to complement a diphthamide mutant strain, and thus probably functions in diphthamide biosynthesis. Diphthamide is a post-translationally modified histidine residue present in elongation factor 2 (EF2) that is the target of diphtheria toxin ADP-ribosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ENSG00000285649 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.26690817).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001319171.2. 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
	DPH2	NM_001384.5	MANE Select	c.268G>T	p.Val90Leu	missense	Exon 3 of 6	NP_001375.2
	DPH2	NM_001319171.2		c.-208G>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 6	NP_001306100.1
	DPH2	NM_001319167.2		c.-312G>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 6	NP_001306096.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPH2	ENST00000255108.8	TSL:1 MANE Select	c.268G>T	p.Val90Leu	missense	Exon 3 of 6	ENSP00000255108.3	Q9BQC3-1
	DPH2	ENST00000922599.1		c.286G>T	p.Val96Leu	missense	Exon 3 of 6	ENSP00000592658.1
	DPH2	ENST00000955917.1		c.268G>T	p.Val90Leu	missense	Exon 3 of 6	ENSP00000625976.1

Frequencies

GnomAD3 genomes AF: 0.000191 AC: 29 AN: 152172 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000413 AC: 8 AN: 193810 AF XY: 0.00000967

Gnomad AFR exome AF: 0.000568

Gnomad AMR exome AF: 0.0000361

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000147 AC: 21 AN: 1424700 Hom.: 0 Cov.: 31 AF XY: 0.0000156 AC XY: 11 AN XY: 705272

African (AFR) AF: 0.000516 AC: 17 AN: 32958

American (AMR) AF: 0.0000260 AC: 1 AN: 38454

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25446

East Asian (EAS) AF: 0.00 AC: 0 AN: 38396

South Asian (SAS) AF: 0.00 AC: 0 AN: 81760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50920

Middle Eastern (MID) AF: 0.000350 AC: 2 AN: 5722

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1091996

Other (OTH) AF: 0.0000169 AC: 1 AN: 59048

GnomAD4 genome AF: 0.000191 AC: 29 AN: 152172 Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11 AN XY: 74332

African (AFR) AF: 0.000676 AC: 28 AN: 41448

American (AMR) AF: 0.0000654 AC: 1 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68012

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.000197 Hom.: 0

Bravo AF: 0.000246

ExAC AF: 0.0000415 AC: 5

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.34
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.24	T
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.17
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.88	D
M_CAP	Benign	0.040	D
MetaRNN	Benign	0.27	T
MetaSVM	Benign	-0.80	T
MutationAssessor	Pathogenic	3.5	H
PhyloP100		4.8
PrimateAI	Uncertain	0.59	T
PROVEAN	Uncertain	-2.5	D
REVEL	Benign	0.18
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.016	D
Polyphen		0.25	B
Vest4		0.40
MutPred		0.52		Gain of helix (P = 0.1736)
MVP		0.64
MPC		0.57
ClinPred		0.29	T
GERP RS		2.9
PromoterAI		0.012	Neutral
Varity_R		0.26
gMVP		0.89
Mutation Taster		=64/36	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs760762295; hg19: chr1-44436645;