chr3-152817576-T-C

Variant names:

• chr3-152817576-T-C
• rs10513432

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 6 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17451 AN: 152066 Hom.: 1901 Cov.: 32

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.: 32 AF XY: 0.114 AC XY: 8472 AN XY: 74426

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: 95 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: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0397 AC: 2702 AN: 68020

Other (OTH) AF: 0.0915 AC: 193 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10513432; hg19: chr3-152535365;