rs3885922

Variant names:

• chr20-6987083-A-G
• rs3885922

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 0.107 in 148,078 control chromosomes in the GnomAD database, including 1,378 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 0.11 (1378 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.107 AC: 15859 AN: 147966 Hom.: 1370 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0344

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0458

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 15893 AN: 148078 Hom.: 1378 Cov.: 31 AF XY: 0.107 AC XY: 7762 AN XY: 72408

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0585

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0458

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0690 Hom.: 180

Bravo AF: 0.115

Asia WGS AF: 0.206 AC: 715 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3885922; hg19: chr20-6967730;