rs10485818

Variant names:

• chr20-239662-A-C
• rs10485818

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.175 in 152,070 control chromosomes in the GnomAD database, including 2,725 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 0.18 (2725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.175 AC: 26627 AN: 151952 Hom.: 2724 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.175 AC: 26632 AN: 152070 Hom.: 2725 Cov.: 32 AF XY: 0.175 AC XY: 13003 AN XY: 74330

African (AFR) AF: 0.289 AC: 11985 AN: 41436

American (AMR) AF: 0.138 AC: 2106 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.191 AC: 989 AN: 5172

South Asian (SAS) AF: 0.201 AC: 970 AN: 4818

European-Finnish (FIN) AF: 0.153 AC: 1622 AN: 10568

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8291 AN: 67996

Other (OTH) AF: 0.142 AC: 300 AN: 2116

Alfa AF: 0.134 Hom.: 6520

Bravo AF: 0.176

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10485818; hg19: chr20-220303;