1-111450602-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001688.5(ATP5PB):​c.77+729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,050 control chromosomes in the GnomAD database, including 19,565 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 0.49 ( 19565 hom., cov: 32)

Consequence

ATP5PB
NM_001688.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.103
Variant links:
Genes affected
ATP5PB (HGNC:840): (ATP synthase peripheral stalk-membrane subunit b) This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the b subunit of the proton channel. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATP5PBNM_001688.5 linkuse as main transcriptc.77+729C>T intron_variant ENST00000369722.8 NP_001679.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATP5PBENST00000369722.8 linkuse as main transcriptc.77+729C>T intron_variant 1 NM_001688.5 ENSP00000358737 P1

Frequencies

GnomAD3 genomes
AF:
0.490
AC:
74443
AN:
151932
Hom.:
19536
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.657
Gnomad AMI
AF:
0.322
Gnomad AMR
AF:
0.335
Gnomad ASJ
AF:
0.295
Gnomad EAS
AF:
0.744
Gnomad SAS
AF:
0.615
Gnomad FIN
AF:
0.453
Gnomad MID
AF:
0.360
Gnomad NFE
AF:
0.414
Gnomad OTH
AF:
0.459
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.490
AC:
74526
AN:
152050
Hom.:
19565
Cov.:
32
AF XY:
0.495
AC XY:
36777
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.657
Gnomad4 AMR
AF:
0.334
Gnomad4 ASJ
AF:
0.295
Gnomad4 EAS
AF:
0.744
Gnomad4 SAS
AF:
0.615
Gnomad4 FIN
AF:
0.453
Gnomad4 NFE
AF:
0.414
Gnomad4 OTH
AF:
0.457
Alfa
AF:
0.431
Hom.:
7506
Bravo
AF:
0.483
Asia WGS
AF:
0.619
AC:
2152
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
6.0
DANN
Benign
0.48

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.

Other links and lift over

dbSNP: rs1264897; hg19: chr1-111993224; API