rs10520563

Variant names:

• chr4-184570684-A-G
• rs10520563

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 0.332 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.515 AC: 21377 AN: 41470

American (AMR) AF: 0.230 AC: 3519 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 858 AN: 3466

East Asian (EAS) AF: 0.0637 AC: 330 AN: 5178

South Asian (SAS) AF: 0.288 AC: 1391 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1944 AN: 10586

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19937 AN: 67964

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.304 Hom.: 33940

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
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10520563; hg19: chr4-185491838;