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

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.

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: 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

Gnomad4 AFR AF: 0.138 AC: 0.138386 AN: 0.138386

Gnomad4 AMR AF: 0.148 AC: 0.147637 AN: 0.147637

Gnomad4 ASJ AF: 0.154 AC: 0.154446 AN: 0.154446

Gnomad4 EAS AF: 0.282 AC: 0.281867 AN: 0.281867

Gnomad4 SAS AF: 0.262 AC: 0.261519 AN: 0.261519

Gnomad4 FIN AF: 0.170 AC: 0.169594 AN: 0.169594

Gnomad4 NFE AF: 0.190 AC: 0.189938 AN: 0.189938

Gnomad4 OTH AF: 0.175 AC: 0.174716 AN: 0.174716

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485662; hg19: chr20-38475206;