rs219683

Variant names:

• chr21-26361267-A-G
• rs219683

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 0.165 in 152,156 control chromosomes in the GnomAD database, including 2,189 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 0.16 (2189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.165 AC: 25032 AN: 152038 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.165 AC: 25045 AN: 152156 Hom.: 2189 Cov.: 32 AF XY: 0.162 AC XY: 12040 AN XY: 74374

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0959

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.154

Alfa AF: 0.161 Hom.: 2233

Bravo AF: 0.164

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219683; hg19: chr21-27733586;