rs10520888

chr5-23280430-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 0.187 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;