chr17-2042400-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000571710.6(DPH1):​c.*543C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,255,722 control chromosomes in the GnomAD database, including 20,588 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1965 hom., cov: 32)
Exomes 𝑓: 0.18 ( 18623 hom. )

Consequence

DPH1
ENST00000571710.6 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0540
Variant links:
Genes affected
DPH1 (HGNC:3003): (diphthamide biosynthesis 1) The protein encoded by this gene is an enzyme involved in the biosynthesis of diphthamide, a modified histidine found only in elongation factor-2 (EEF2). Diphthamide residues in EEF2 are targeted for ADP-ribosylation by diphtheria toxin and Pseudomonas exotoxin A. Defects in this gene have been associated with both ovarian cancer and autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. [provided by RefSeq, Oct 2016]
OVCA2 (HGNC:24203): (OVCA2 serine hydrolase domain containing) Involved in response to retinoic acid. Located in cytoplasm. Biomarker of ovarian cancer. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 17-2042400-C-T is Benign according to our data. Variant chr17-2042400-C-T is described in ClinVar as [Benign]. Clinvar id is 1302080.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DPH1NM_001383.6 linkuse as main transcriptc.*19-205C>T intron_variant ENST00000263083.12 NP_001374.4
OVCA2NM_080822.3 linkuse as main transcriptc.184+169C>T intron_variant ENST00000572195.3 NP_543012.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DPH1ENST00000263083.12 linkuse as main transcriptc.*19-205C>T intron_variant 1 NM_001383.6 ENSP00000263083 P1Q9BZG8-4
OVCA2ENST00000572195.3 linkuse as main transcriptc.184+169C>T intron_variant 1 NM_080822.3 ENSP00000461388 P1

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21947
AN:
152042
Hom.:
1966
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0526
Gnomad AMI
AF:
0.303
Gnomad AMR
AF:
0.142
Gnomad ASJ
AF:
0.241
Gnomad EAS
AF:
0.0593
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.192
Gnomad OTH
AF:
0.177
GnomAD4 exome
AF:
0.178
AC:
195917
AN:
1103562
Hom.:
18623
Cov.:
17
AF XY:
0.176
AC XY:
94329
AN XY:
536020
show subpopulations
Gnomad4 AFR exome
AF:
0.0475
Gnomad4 AMR exome
AF:
0.125
Gnomad4 ASJ exome
AF:
0.245
Gnomad4 EAS exome
AF:
0.0381
Gnomad4 SAS exome
AF:
0.100
Gnomad4 FIN exome
AF:
0.209
Gnomad4 NFE exome
AF:
0.188
Gnomad4 OTH exome
AF:
0.181
GnomAD4 genome
AF:
0.144
AC:
21942
AN:
152160
Hom.:
1965
Cov.:
32
AF XY:
0.144
AC XY:
10723
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0525
Gnomad4 AMR
AF:
0.142
Gnomad4 ASJ
AF:
0.241
Gnomad4 EAS
AF:
0.0594
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.192
Gnomad4 OTH
AF:
0.175
Alfa
AF:
0.177
Hom.:
536
Bravo
AF:
0.137
Asia WGS
AF:
0.0970
AC:
338
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJul 29, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
4.5
DANN
Benign
0.61

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs55815331; hg19: chr17-1945694; API