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GeneBe

rs768000

chr1-36091266-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_017825.3(ADPRS):c.234C>T(p.Asp78=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 1,614,118 control chromosomes in the GnomAD database, including 1,359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 241 hom., cov: 33)
Exomes 𝑓: 0.012 ( 1118 hom. )

Consequence

ADPRS
NM_017825.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.11
Variant links:
Genes affected
ADPRS (HGNC:21304): (ADP-ribosylserine hydrolase) This gene encodes a member of the ADP-ribosylglycohydrolase family. The encoded enzyme catalyzes the removal of ADP-ribose from ADP-ribosylated proteins. This enzyme localizes to the mitochondria, in addition to the nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-36091266-C-T is Benign according to our data. Variant chr1-36091266-C-T is described in ClinVar as [Benign]. Clinvar id is 3058872.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=3.11 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADPRSNM_017825.3 linkuse as main transcriptc.234C>T p.Asp78= synonymous_variant 2/6 ENST00000373178.5
ADPRSXM_011541636.3 linkuse as main transcriptc.-154-352C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADPRSENST00000373178.5 linkuse as main transcriptc.234C>T p.Asp78= synonymous_variant 2/61 NM_017825.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0305
AC:
4636
AN:
152198
Hom.:
241
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0574
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0334
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.234
Gnomad SAS
AF:
0.0118
Gnomad FIN
AF:
0.0267
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00194
Gnomad OTH
AF:
0.0253
GnomAD3 exomes
AF:
0.0327
AC:
8222
AN:
251226
Hom.:
611
AF XY:
0.0284
AC XY:
3859
AN XY:
135812
show subpopulations
Gnomad AFR exome
AF:
0.0606
Gnomad AMR exome
AF:
0.0454
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.240
Gnomad SAS exome
AF:
0.00614
Gnomad FIN exome
AF:
0.0301
Gnomad NFE exome
AF:
0.00247
Gnomad OTH exome
AF:
0.0213
GnomAD4 exome
AF:
0.0116
AC:
16984
AN:
1461802
Hom.:
1118
Cov.:
31
AF XY:
0.0111
AC XY:
8038
AN XY:
727206
show subpopulations
Gnomad4 AFR exome
AF:
0.0565
Gnomad4 AMR exome
AF:
0.0457
Gnomad4 ASJ exome
AF:
0.000344
Gnomad4 EAS exome
AF:
0.206
Gnomad4 SAS exome
AF:
0.00781
Gnomad4 FIN exome
AF:
0.0272
Gnomad4 NFE exome
AF:
0.00114
Gnomad4 OTH exome
AF:
0.0235
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0305
AC:
4646
AN:
152316
Hom.:
241
Cov.:
33
AF XY:
0.0323
AC XY:
2405
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0574
Gnomad4 AMR
AF:
0.0339
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.234
Gnomad4 SAS
AF:
0.0118
Gnomad4 FIN
AF:
0.0267
Gnomad4 NFE
AF:
0.00193
Gnomad4 OTH
AF:
0.0251
Alfa
AF:
0.00897
Hom.:
68
Bravo
AF:
0.0339
Asia WGS
AF:
0.102
AC:
352
AN:
3478
EpiCase
AF:
0.00104
EpiControl
AF:
0.00196

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

ADPRS-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesMar 20, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
11
Dann
Benign
0.88

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: rs768000; hg19: chr1-36556867; COSMIC: COSV52881466; COSMIC: COSV52881466; API