Genetic Variant ATAD3B:p.Glu66Glu (chr1-1472082-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_031921.6(ATAD3B):c.198G>A(p.Glu66Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00197 in 139,668 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0020 ( 2 hom., cov: 25)

Exomes 𝑓: 0.00016 ( 3 hom. )

Failed GnomAD Quality Control

Consequence

ATAD3B
NM_031921.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.88

Publications

0 publications found

Variant links:

Genes affected

ATAD3B (HGNC:24007): (ATPase family AAA domain containing 3B) The protein encoded by this gene is localized to the mitochondrial inner membrane, where it can bind to a highly-related protein, ATAD3A. ATAD3A appears to interact with matrix nucleoid complexes, and the encoded protein negatively regulates that interaction. This gene is expressed almost exclusively in pluripotent embryonic stem cells and some cancer cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

ATAD3B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BS2

High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031921.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATAD3B	NM_031921.6	MANE Select	c.198G>A	p.Glu66Glu	synonymous	Exon 1 of 16	NP_114127.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ATAD3B	ENST00000673477.1	MANE Select	c.198G>A	p.Glu66Glu	synonymous	Exon 1 of 16	ENSP00000500094.1	Q5T9A4-1
ATAD3B	ENST00000308647.8	TSL:1	c.198G>A	p.Glu66Glu	synonymous	Exon 1 of 14	ENSP00000311766.8	A0A5K1VW56
ATAD3B	ENST00000940534.1		c.198G>A	p.Glu66Glu	synonymous	Exon 1 of 17	ENSP00000610593.1

Frequencies

GnomAD3 genomes

AF:

0.00197

AC:

275

AN:

139598

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00736

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000704

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000603

Gnomad OTH

AF:

0.00206

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000165

AC:

174

AN:

1056212

Hom.:

Cov.:

AF XY:

0.000170

AC XY:

AN XY:

500560

show subpopulations

African (AFR)

AF:

0.00664

AC:

139

AN:

20924

American (AMR)

AF:

0.000298

AC:

AN:

6722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12340

East Asian (EAS)

AF:

0.00

AC:

AN:

20900

South Asian (SAS)

AF:

0.0000405

AC:

AN:

24704

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27592

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2652

European-Non Finnish (NFE)

AF:

0.0000111

AC:

AN:

899542

Other (OTH)

AF:

0.000539

AC:

AN:

40836

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.420

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00197

AC:

275

AN:

139668

Hom.:

Cov.:

AF XY:

0.00189

AC XY:

128

AN XY:

67868

show subpopulations

African (AFR)

AF:

0.00734

AC:

257

AN:

35022

American (AMR)

AF:

0.000703

AC:

AN:

14216

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3400

East Asian (EAS)

AF:

0.00

AC:

AN:

3996

South Asian (SAS)

AF:

0.00

AC:

AN:

4262

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9370

Middle Eastern (MID)

AF:

0.00

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.0000603

AC:

AN:

66286

Other (OTH)

AF:

0.00204

AC:

AN:

1958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Uncertain

0.98

PhyloP100

3.9

PromoterAI

0.050

Neutral

(source)

Mutation Taster

=292/8

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over