chr1-46643579-A-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.72

Publications

6 publications found
Variant links:
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]

Genome browser will be placed here

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
ATPAF1NM_001394565.1 linkc.685-278T>C intron_variant Intron 7 of 8 ENST00000574428.6 NP_001381494.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATPAF1ENST00000574428.6 linkc.685-278T>C intron_variant Intron 7 of 8 1 NM_001394565.1 ENSP00000459167.2 Q5TC12-1

Frequencies

GnomAD3 genomes
AF:
0.877
AC:
133452
AN:
152168
Hom.:
60280
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.663
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.934
Gnomad ASJ
AF:
0.987
Gnomad EAS
AF:
0.604
Gnomad SAS
AF:
0.857
Gnomad FIN
AF:
0.962
Gnomad MID
AF:
0.959
Gnomad NFE
AF:
0.995
Gnomad OTH
AF:
0.909
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.877
AC:
133514
AN:
152286
Hom.:
60291
Cov.:
33
AF XY:
0.873
AC XY:
65030
AN XY:
74452
show subpopulations
African (AFR)
AF:
0.663
AC:
27514
AN:
41522
American (AMR)
AF:
0.934
AC:
14289
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
0.987
AC:
3424
AN:
3470
East Asian (EAS)
AF:
0.604
AC:
3132
AN:
5182
South Asian (SAS)
AF:
0.857
AC:
4138
AN:
4828
European-Finnish (FIN)
AF:
0.962
AC:
10213
AN:
10614
Middle Eastern (MID)
AF:
0.956
AC:
281
AN:
294
European-Non Finnish (NFE)
AF:
0.995
AC:
67703
AN:
68044
Other (OTH)
AF:
0.903
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:
0.948
Hom.:
26931
Bravo
AF:
0.866
Asia WGS
AF:
0.706
AC:
2458
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
15
DANN
Benign
0.86
PhyloP100
2.7
Mutation Taster
=99/1
polymorphism (auto)

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

Other links and lift over

dbSNP: rs1273237; hg19: chr1-47109251; API