rs219683

Positions:

• chr21-26361267-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 0.165 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;