rs928862

Positions:

• chr21-20265406-A-G

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 0.148 in 152,158 control chromosomes in the GnomAD database, including 2,186 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 0.15 (2186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22529 AN: 152040 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.148 AC: 22536 AN: 152158 Hom.: 2186 Cov.: 32 AF XY: 0.151 AC XY: 11258 AN XY: 74400

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.143

Alfa AF: 0.172 Hom.: 2185

Bravo AF: 0.149

Asia WGS AF: 0.184 AC: 639 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928862; hg19: chr21-21637719;