rs10485820

Variant names:

• chr20-617634-T-C
• rs10485820

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 0.174 in 152,058 control chromosomes in the GnomAD database, including 2,657 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 0.17 (2657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.174 AC: 26393 AN: 151940 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.174 AC: 26409 AN: 152058 Hom.: 2657 Cov.: 32 AF XY: 0.167 AC XY: 12411 AN XY: 74346

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0922

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.194

Alfa AF: 0.195 Hom.: 1203

Bravo AF: 0.172

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
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: rs10485820; hg19: chr20-598278;