rs10485753

Variant names:

• chr20-12457608-G-A
• rs10485753

Your query was ambiguous. Multiple possible variants found:

• chr20-12457608-G-A
• chr20-12457608-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 0.0948 in 152,010 control chromosomes in the GnomAD database, including 758 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 0.095 (758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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: 0.0948 AC: 14397 AN: 151892 Hom.: 758 Cov.: 33

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0948 AC: 14406 AN: 152010 Hom.: 758 Cov.: 33 AF XY: 0.0961 AC XY: 7141 AN XY: 74312

African (AFR) AF: 0.0617 AC: 2561 AN: 41490

American (AMR) AF: 0.121 AC: 1848 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3462

East Asian (EAS) AF: 0.136 AC: 700 AN: 5166

South Asian (SAS) AF: 0.132 AC: 636 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1067 AN: 10578

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6995 AN: 67928

Other (OTH) AF: 0.0807 AC: 170 AN: 2106

Alfa AF: 0.0813 Hom.: 141

Bravo AF: 0.0934

Asia WGS AF: 0.0990 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.38
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10485753; hg19: chr20-12438256;