rs10485662

Variant names:

• chr20-39846564-G-A
• rs10485662

Your query was ambiguous. Multiple possible variants found:

• chr20-39846564-G-A
• chr20-39846564-G-C

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 152,104 control chromosomes in the GnomAD database, including 2,412 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 (2412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26565 AN: 151986 Hom.: 2409 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.175 AC: 26587 AN: 152104 Hom.: 2412 Cov.: 32 AF XY: 0.176 AC XY: 13114 AN XY: 74360

African (AFR) AF: 0.138 AC: 5743 AN: 41500

American (AMR) AF: 0.148 AC: 2255 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3464

East Asian (EAS) AF: 0.282 AC: 1455 AN: 5162

South Asian (SAS) AF: 0.262 AC: 1260 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1796 AN: 10590

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12912 AN: 67980

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.184 Hom.: 4436

Bravo AF: 0.169

Asia WGS AF: 0.294 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.70
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10485662; hg19: chr20-38475206;