rs10520888

Variant names:

• chr5-23280430-A-G
• rs10520888

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 0.187 in 151,508 control chromosomes in the GnomAD database, including 2,938 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 0.19 (2938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 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: 0.187 AC: 28248 AN: 151392 Hom.: 2917 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.187 AC: 28310 AN: 151508 Hom.: 2938 Cov.: 32 AF XY: 0.190 AC XY: 14075 AN XY: 74014

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.206

Alfa AF: 0.161 Hom.: 1056

Bravo AF: 0.189

Asia WGS AF: 0.342 AC: 1185 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.44
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520888; hg19: chr5-23280539;