rs10485813

Variant names:

• chr20-52967444-A-G
• rs10485813

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 0.129 in 152,240 control chromosomes in the GnomAD database, including 1,570 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 0.13 (1570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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: 0.129 AC: 19560 AN: 152122 Hom.: 1564 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.129 AC: 19576 AN: 152240 Hom.: 1570 Cov.: 32 AF XY: 0.131 AC XY: 9729 AN XY: 74446

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0971 Hom.: 588

Bravo AF: 0.141

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485813; hg19: chr20-51583983;