rs10485620

Variant names:

• chr20-51948629-T-C
• rs10485620

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 0.192 in 152,032 control chromosomes in the GnomAD database, including 3,033 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 (3033 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 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: 0.192 AC: 29196 AN: 151912 Hom.: 3021 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.192 AC: 29247 AN: 152032 Hom.: 3033 Cov.: 32 AF XY: 0.194 AC XY: 14397 AN XY: 74298

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0914

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.182

Alfa AF: 0.184 Hom.: 5342

Bravo AF: 0.202

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485620; hg19: chr20-50565168;