rs10485820

Variant names:

• chr20-617634-T-C
• rs10485820

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 0.174 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.109 AC: 4520 AN: 41452

American (AMR) AF: 0.169 AC: 2581 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.0922 AC: 445 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10572

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15348 AN: 67968

Other (OTH) AF: 0.194 AC: 410 AN: 2114

Alfa AF: 0.193 Hom.: 1937

Bravo AF: 0.172

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs10485820; hg19: chr20-598278;