Variant chr17-30834972-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_024857.5(ATAD5):c.891C>T(p.Asp297=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 1,613,892 control chromosomes in the GnomAD database, including 761 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.019 ( 43 hom., cov: 33)

Exomes 𝑓: 0.027 ( 718 hom. )

Consequence

ATAD5
NM_024857.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0450

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:

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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=-0.81).

BP6

Variant 17-30834972-C-T is Benign according to our data. Variant chr17-30834972-C-T is described in ClinVar as [Benign]. Clinvar id is 3055573.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.045 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0569 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.891C>T	p.Asp297=	synonymous_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.891C>T	p.Asp297=	synonymous_variant	2/23	1	NM_024857.5	P1	Q96QE3-1
ATAD5	ENST00000578295.5 linkuse as main transcript	c.891C>T	p.Asp297=	synonymous_variant	2/15	1
	ENST00000580873.1 linkuse as main transcript	n.334-343G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0189

AC:

2872

AN:

152042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00505

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0126

Gnomad ASJ

AF:

0.0505

Gnomad EAS

AF:

0.000768

Gnomad SAS

AF:

0.0623

Gnomad FIN

AF:

0.00784

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0269

Gnomad OTH

AF:

0.0263

GnomAD3 exomes

AF:

0.0243

AC:

6081

AN:

250384

Hom.:

147

AF XY:

0.0276

AC XY:

3739

AN XY:

135714

show subpopulations

Gnomad AFR exome

AF:

0.00547

Gnomad AMR exome

AF:

0.0112

Gnomad ASJ exome

AF:

0.0555

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0615

Gnomad FIN exome

AF:

0.00776

Gnomad NFE exome

AF:

0.0251

Gnomad OTH exome

AF:

0.0261

GnomAD4 exome

AF:

0.0266

AC:

38907

AN:

1461732

Hom.:

718

Cov.:

AF XY:

0.0281

AC XY:

20407

AN XY:

727160

show subpopulations

Gnomad4 AFR exome

AF:

0.00445

Gnomad4 AMR exome

AF:

0.0121

Gnomad4 ASJ exome

AF:

0.0563

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0620

Gnomad4 FIN exome

AF:

0.00742

Gnomad4 NFE exome

AF:

0.0260

Gnomad4 OTH exome

AF:

0.0292

GnomAD4 genome

AF:

0.0189

AC:

2871

AN:

152160

Hom.:

Cov.:

AF XY:

0.0188

AC XY:

1397

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.00504

Gnomad4 AMR

AF:

0.0126

Gnomad4 ASJ

AF:

0.0505

Gnomad4 EAS

AF:

0.000770

Gnomad4 SAS

AF:

0.0627

Gnomad4 FIN

AF:

0.00784

Gnomad4 NFE

AF:

0.0269

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0212

Hom.:

Bravo

AF:

0.0184

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0287

EpiControl

AF:

0.0294

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

Feb 19, 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

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.2

DANN

Benign

0.85

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