Variant 13-113422857-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001394807.1(ADPRHL1):c.1030G>A(p.Ala344Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00626 in 1,612,906 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0065 ( 41 hom. )

Consequence

ADPRHL1
NM_001394807.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.81

Variant links:

Genes affected

ADPRHL1 (HGNC:21303): (ADP-ribosylhydrolase like 1) ADP-ribosylation is a reversible posttranslational modification used to regulate protein function. ADP-ribosyltransferases (see ART1; MIM 601625) transfer ADP-ribose from NAD+ to the target protein, and ADP-ribosylhydrolases, such as ADPRHL1, reverse the reaction (Glowacki et al., 2002 [PubMed 12070318]).[supplied by OMIM, Mar 2008]

ADPRHL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0051038265).

BP6

Variant 13-113422857-C-T is Benign according to our data. Variant chr13-113422857-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644007.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 41 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRHL1	NM_001394807.1 link	c.1030G>A	p.Ala344Thr	missense_variant	7/8	ENST00000612156.3	NP_001381736.1
ADPRHL1	NM_138430.5 link	c.1030G>A	p.Ala344Thr	missense_variant	7/7		NP_612439.2	Q8NDY3-1
ADPRHL1	NM_199162.3 link	c.784G>A	p.Ala262Thr	missense_variant	7/7		NP_954631.1	Q8NDY3-2
ADPRHL1	XM_047430086.1 link	c.784G>A	p.Ala262Thr	missense_variant	7/8		XP_047286042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADPRHL1	ENST00000612156.3 link	c.1030G>A	p.Ala344Thr	missense_variant	7/8	5	NM_001394807.1	ENSP00000489048.1	A0A0U1RQK4
ADPRHL1	ENST00000375418.8 link	c.1030G>A	p.Ala344Thr	missense_variant	7/7	1		ENSP00000364567.3	Q8NDY3-1
ADPRHL1	ENST00000356501.8 link	c.784G>A	p.Ala262Thr	missense_variant	7/7	1		ENSP00000348894.4	Q8NDY3-2

Frequencies

GnomAD3 genomes

AF:

0.00419

AC:

638

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000893

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00262

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.00264

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00753

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00506

AC:

1265

AN:

250006

Hom.:

AF XY:

0.00537

AC XY:

729

AN XY:

135666

show subpopulations

Gnomad AFR exome

AF:

0.00130

Gnomad AMR exome

AF:

0.00182

Gnomad ASJ exome

AF:

0.000200

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00359

Gnomad FIN exome

AF:

0.00305

Gnomad NFE exome

AF:

0.00868

Gnomad OTH exome

AF:

0.00410

GnomAD4 exome

AF:

0.00647

AC:

9452

AN:

1460602

Hom.:

Cov.:

AF XY:

0.00634

AC XY:

4603

AN XY:

726586

show subpopulations

Gnomad4 AFR exome

AF:

0.000956

Gnomad4 AMR exome

AF:

0.00186

Gnomad4 ASJ exome

AF:

0.000191

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00344

Gnomad4 FIN exome

AF:

0.00324

Gnomad4 NFE exome

AF:

0.00769

Gnomad4 OTH exome

AF:

0.00497

GnomAD4 genome

AF:

0.00419

AC:

638

AN:

152304

Hom.:

Cov.:

AF XY:

0.00424

AC XY:

316

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.000890

Gnomad4 AMR

AF:

0.00261

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.00264

Gnomad4 NFE

AF:

0.00753

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00665

Hom.:

Bravo

AF:

0.00396

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00804

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00593

AC:

ExAC

AF:

0.00541

AC:

655

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00720

EpiControl

AF:

0.00717

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

ADPRHL1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.68

CADD

Benign

8.3

DANN

Benign

0.96

DEOGEN2

Benign

0.0066

T;.;T

Eigen

Benign

-0.81

Eigen_PC

Benign

-0.73

FATHMM_MKL

Uncertain

0.78

LIST_S2

Benign

0.64

T;T;T

M_CAP

Benign

0.0071

MetaRNN

Benign

0.0051

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.64

.;.;N

PrimateAI

Benign

0.20

PROVEAN

Benign

0.17

.;N;N

REVEL

Benign

0.14

Sift

Benign

0.43

.;T;T

Sift4G

Benign

0.76

T;T;T

Polyphen

0.0040

.;.;B

Vest4

0.18

MVP

0.15

MPC

0.088

ClinPred

0.013

GERP RS

1.2

Varity_R

0.073

gMVP

0.095

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