chr1-46652517-G-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394565.1(ATPAF1):​c.588+64C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000464 in 1,293,600 control chromosomes in the GnomAD database, including 1 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: not found (cov: 32)
Exomes 𝑓: 0.0000046 ( 1 hom. )

Consequence

ATPAF1
NM_001394565.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.173

Publications

10 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: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATPAF1NM_001394565.1 linkc.588+64C>T intron_variant Intron 6 of 8 ENST00000574428.6 NP_001381494.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATPAF1ENST00000574428.6 linkc.588+64C>T intron_variant Intron 6 of 8 1 NM_001394565.1 ENSP00000459167.2 Q5TC12-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000464
AC:
6
AN:
1293600
Hom.:
1
Cov.:
21
AF XY:
0.00000770
AC XY:
5
AN XY:
648970
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30070
American (AMR)
AF:
0.00
AC:
0
AN:
41800
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24322
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38470
South Asian (SAS)
AF:
0.0000618
AC:
5
AN:
80934
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52456
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5432
European-Non Finnish (NFE)
AF:
0.00000104
AC:
1
AN:
965370
Other (OTH)
AF:
0.00
AC:
0
AN:
54746
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.7
DANN
Benign
0.93
PhyloP100
-0.17

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: rs620431; hg19: chr1-47118189; API