chr11-73991026-T-C

Variant names:

• chr11-73991026-T-C
• rs653529

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 0.494 in 152,086 control chromosomes in the GnomAD database, including 20,406 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 (20406 hom., cov: 32)
• Consequence: DPPA4P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 12 publications found

Genes affected

DPPA4P3 (HGNC:56531): (DPPA4 pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75134 AN: 151968 Hom.: 20392 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.494 AC: 75193 AN: 152086 Hom.: 20406 Cov.: 32 AF XY: 0.491 AC XY: 36538 AN XY: 74354

African (AFR) AF: 0.745 AC: 30903 AN: 41474

American (AMR) AF: 0.471 AC: 7196 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2222 AN: 5162

South Asian (SAS) AF: 0.360 AC: 1735 AN: 4826

European-Finnish (FIN) AF: 0.405 AC: 4286 AN: 10584

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26288 AN: 67992

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.489 Hom.: 2802

Bravo AF: 0.512

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.42
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs653529; hg19: chr11-73702071;