Variant chr17-30834340-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_024857.5(ATAD5):c.259C>T(p.Pro87Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,609,988 control chromosomes in the GnomAD database, including 13,291 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1452 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11839 hom. )

Consequence

ATAD5
NM_024857.5 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.100

Variant links:

Genes affected

ATAD5 (HGNC:25752): (ATPase family AAA domain containing 5) Enables DNA clamp unloader activity. Involved in DNA clamp unloading; positive regulation of DNA replication; and positive regulation of cell cycle G2/M phase transition. Part of Elg1 RFC-like complex. Biomarker of neurilemmoma. [provided by Alliance of Genome Resources, Apr 2022]

ATAD5 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0027531087).

BP6

Variant 17-30834340-C-T is Benign according to our data. Variant chr17-30834340-C-T is described in ClinVar as [Benign]. Clinvar id is 3059655.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATAD5	NM_024857.5 linkuse as main transcript	c.259C>T	p.Pro87Ser	missense_variant	2/23	ENST00000321990.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATAD5	ENST00000321990.5 linkuse as main transcript	c.259C>T	p.Pro87Ser	missense_variant	2/23	1	NM_024857.5	P1	Q96QE3-1
ATAD5	ENST00000578295.5 linkuse as main transcript	c.259C>T	p.Pro87Ser	missense_variant	2/15	1
	ENST00000580873.1 linkuse as main transcript	n.623G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

19959

AN:

150250

Hom.:

1442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.0875

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.0884

Gnomad MID

AF:

0.0980

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.124

GnomAD3 exomes

AF:

0.137

AC:

34064

AN:

249084

Hom.:

2695

AF XY:

0.138

AC XY:

18574

AN XY:

134650

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.0871

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.247

Gnomad FIN exome

AF:

0.0856

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.119

AC:

174395

AN:

1459614

Hom.:

11839

Cov.:

AF XY:

0.122

AC XY:

88744

AN XY:

726012

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.0890

Gnomad4 EAS exome

AF:

0.161

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.0879

Gnomad4 NFE exome

AF:

0.107

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.133

AC:

20011

AN:

150374

Hom.:

1452

Cov.:

AF XY:

0.134

AC XY:

9875

AN XY:

73484

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.0875

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.0884

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.111

Hom.:

2585

Bravo

AF:

0.136

TwinsUK

AF:

0.108

AC:

402

ALSPAC

AF:

0.105

AC:

403

ESP6500AA

AF:

0.166

AC:

730

ESP6500EA

AF:

0.105

AC:

902

ExAC

AF:

0.140

AC:

16974

Asia WGS

AF:

0.195

AC:

678

AN:

3478

EpiCase

AF:

0.103

EpiControl

AF:

0.103

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ATAD5-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 2019

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

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.73

DANN

Benign

0.61

DEOGEN2

Benign

0.028

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0076

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0028

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-2.3

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Benign

1.4

REVEL

Benign

0.043

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.036

MPC

0.070

ClinPred

0.0030

GERP RS

1.4

Varity_R

0.025

gMVP

0.043

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