chr1-46643579-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001394565.1(ATPAF1):c.685-278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,286 control chromosomes in the GnomAD database, including 60,291 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 0.88 ( 60291 hom., cov: 33)
Consequence
ATPAF1
NM_001394565.1 intron
NM_001394565.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.72
Publications
6 publications found
Genes affected
ATPAF1 (HGNC:18803): (ATP synthase mitochondrial F1 complex assembly factor 1) This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 beta subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATPAF1 | NM_001394565.1 | c.685-278T>C | intron_variant | Intron 7 of 8 | ENST00000574428.6 | NP_001381494.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.877 AC: 133452AN: 152168Hom.: 60280 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
133452
AN:
152168
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.877 AC: 133514AN: 152286Hom.: 60291 Cov.: 33 AF XY: 0.873 AC XY: 65030AN XY: 74452 show subpopulations
GnomAD4 genome
AF:
AC:
133514
AN:
152286
Hom.:
Cov.:
33
AF XY:
AC XY:
65030
AN XY:
74452
show subpopulations
African (AFR)
AF:
AC:
27514
AN:
41522
American (AMR)
AF:
AC:
14289
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
AC:
3424
AN:
3470
East Asian (EAS)
AF:
AC:
3132
AN:
5182
South Asian (SAS)
AF:
AC:
4138
AN:
4828
European-Finnish (FIN)
AF:
AC:
10213
AN:
10614
Middle Eastern (MID)
AF:
AC:
281
AN:
294
European-Non Finnish (NFE)
AF:
AC:
67703
AN:
68044
Other (OTH)
AF:
AC:
1908
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
663
1326
1990
2653
3316
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
882
1764
2646
3528
4410
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2458
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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