Genetic Variant ADPRS:p.Asp78Asp (chr1-36091266-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_017825.3(ADPRS):c.234C>T(p.Asp78Asp) 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 (no stars).

Frequency

Genomes: 𝑓 0.031 ( 241 hom., cov: 33)

Exomes 𝑓: 0.012 ( 1118 hom. )

Consequence

ADPRS
NM_017825.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

ADPRS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=3.11 with no splicing effect.

BA1

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 rank	MANE	Protein	UniProt
ADPRS	NM_017825.3 link	c.234C>T	p.Asp78Asp	synonymous_variant	Exon 2 of 6	ENST00000373178.5	NP_060295.1	Q9NX46
ADPRS	XM_011541636.3 link	c.-154-352C>T		intron_variant	Intron 1 of 4		XP_011539938.1	B7ZAN4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADPRS	ENST00000373178.5 link	c.234C>T	p.Asp78Asp	synonymous_variant	Exon 2 of 6	1	NM_017825.3	ENSP00000362273.4		Q9NX46

Frequencies

GnomAD3 genomes

AF:

0.0305

AC:

4636

AN:

152198

Hom.:

241

Cov.:

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.:

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

AF:

0.0305

AC:

4646

AN:

152316

Hom.:

241

Cov.:

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.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

ADPRS-related disorder

Benign:1

Mar 20, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This 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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over