Genetic Variant ATAD5:p.Pro13Pro (chr17-30832386-G-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_024857.5(ATAD5):c.39G>C(p.Pro13Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,558,698 control chromosomes in the GnomAD database, including 22,406 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 6144 hom., cov: 32)

Exomes 𝑓: 0.13 ( 16262 hom. )

Consequence

ATAD5
NM_024857.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0680

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 17-30832386-G-C is Benign according to our data. Variant chr17-30832386-G-C is described in ClinVar as [Benign]. Clinvar id is 3059114.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.068 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATAD5	NM_024857.5 link	c.39G>C	p.Pro13Pro	synonymous_variant	Exon 1 of 23	ENST00000321990.5	NP_079133.3	Q96QE3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATAD5	ENST00000321990.5 link	c.39G>C	p.Pro13Pro	synonymous_variant	Exon 1 of 23	1	NM_024857.5	ENSP00000313171.4		Q96QE3-1
ATAD5	ENST00000578295.5 link	n.39G>C		non_coding_transcript_exon_variant	Exon 1 of 15	1		ENSP00000463102.1		A0A075B754

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35025

AN:

151892

Hom.:

6107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.0952

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.0943

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.201

GnomAD3 exomes

AF:

0.162

AC:

34700

AN:

213678

Hom.:

3968

AF XY:

0.158

AC XY:

18417

AN XY:

116356

show subpopulations

Gnomad AFR exome

AF:

0.493

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.0917

Gnomad EAS exome

AF:

0.121

Gnomad SAS exome

AF:

0.271

Gnomad FIN exome

AF:

0.0912

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.133

AC:

187322

AN:

1406688

Hom.:

16262

Cov.:

AF XY:

0.135

AC XY:

94609

AN XY:

699186

show subpopulations

Gnomad4 AFR exome

AF:

0.496

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.0942

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.269

Gnomad4 FIN exome

AF:

0.0925

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.152

GnomAD4 genome

AF:

0.231

AC:

35125

AN:

152010

Hom.:

6144

Cov.:

AF XY:

0.229

AC XY:

17022

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.209

Gnomad4 ASJ

AF:

0.0952

Gnomad4 EAS

AF:

0.131

Gnomad4 SAS

AF:

0.269

Gnomad4 FIN

AF:

0.0943

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.203

Alfa

AF:

0.132

Hom.:

1345

Bravo

AF:

0.248

Asia WGS

AF:

0.234

AC:

813

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ATAD5-related disorder

Benign:1

Oct 18, 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

-0.55

CADD

Benign

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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