rs10520563

Positions:

• chr4-184570684-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.332 in 152,100 control chromosomes in the GnomAD database, including 9,489 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 0.33 (9489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50354 AN: 151982 Hom.: 9463 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.332 AC: 50426 AN: 152100 Hom.: 9489 Cov.: 32 AF XY: 0.322 AC XY: 23973 AN XY: 74344

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.334

Alfa AF: 0.299 Hom.: 15215

Bravo AF: 0.339

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520563; hg19: chr4-185491838;