rs10485810

Variant names:

• chr20-57946227-A-G
• rs10485810

Your query was ambiguous. Multiple possible variants found:

• chr20-57946227-A-G
• chr20-57946227-A-T

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 0.0414 in 152,322 control chromosomes in the GnomAD database, including 178 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 0.041 (178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0595 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: 0.0415 AC: 6314 AN: 152204 Hom.: 178 Cov.: 32

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0266

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0414 AC: 6312 AN: 152322 Hom.: 178 Cov.: 32 AF XY: 0.0413 AC XY: 3079 AN XY: 74474

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0443 Hom.: 93

Bravo AF: 0.0362

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.78
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485810; hg19: chr20-56521283;