21-19692305-A-G

Variant names:

• chr21-19692305-A-G
• rs218322

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 0.241 in 151,968 control chromosomes in the GnomAD database, including 5,170 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 0.24 (5170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.241 AC: 36592 AN: 151852 Hom.: 5161 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.241 AC: 36644 AN: 151968 Hom.: 5170 Cov.: 32 AF XY: 0.242 AC XY: 17952 AN XY: 74286

African (AFR) AF: 0.395 AC: 16359 AN: 41432

American (AMR) AF: 0.243 AC: 3705 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1402 AN: 5156

South Asian (SAS) AF: 0.185 AC: 893 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1783 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11260 AN: 67954

Other (OTH) AF: 0.262 AC: 554 AN: 2114

Alfa AF: 0.182 Hom.: 3622

Bravo AF: 0.255

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.84
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs218322; hg19: chr21-21064619;