dbSNP rs10513432: ATP5MGP5:n.152817576T>C (chr3-152817576-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.115 in 152,184 control chromosomes in the GnomAD database, including 1,909 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 0.11 ( 1909 hom., cov: 32)

Consequence

ATP5MGP5
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.274

Publications

6 publications found

Variant links:

Genes affected

ATP5MGP5 (HGNC:38167): (ATP synthase membrane subunit g pseudogene 5)

ATP5MGP5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP5MGP5		n.152817576T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17451

AN:

152066

Hom.:

1901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.0541

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.0331

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0676

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0397

Gnomad OTH

AF:

0.0929

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.115

AC:

17500

AN:

152184

Hom.:

1909

Cov.:

AF XY:

0.114

AC XY:

8472

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.295

AC:

12221

AN:

41456

American (AMR)

AF:

0.0540

AC:

825

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0274

AC:

AN:

3470

East Asian (EAS)

AF:

0.0330

AC:

171

AN:

5182

South Asian (SAS)

AF:

0.100

AC:

484

AN:

4832

European-Finnish (FIN)

AF:

0.0676

AC:

718

AN:

10618

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0397

AC:

2702

AN:

68020

Other (OTH)

AF:

0.0915

AC:

193

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

694

1388

2083

2777

3471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0607

Hom.:

2625

Bravo

AF:

0.122

Asia WGS

AF:

0.0900

AC:

316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.6

(source)

DANN

Benign

0.49

PhyloP100

-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs10513432

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over