21-21881735-A-G

Variant names:

• chr21-21881735-A-G
• rs2827107

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 0.275 in 151,978 control chromosomes in the GnomAD database, including 6,186 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 0.28 (6186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41822 AN: 151858 Hom.: 6192 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.275 AC: 41847 AN: 151978 Hom.: 6186 Cov.: 32 AF XY: 0.279 AC XY: 20744 AN XY: 74306

African (AFR) AF: 0.304 AC: 12607 AN: 41470

American (AMR) AF: 0.282 AC: 4302 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3220 AN: 5154

South Asian (SAS) AF: 0.345 AC: 1665 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2542 AN: 10584

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15795 AN: 67914

Other (OTH) AF: 0.275 AC: 581 AN: 2110

Alfa AF: 0.247 Hom.: 7321

Bravo AF: 0.281

Asia WGS AF: 0.449 AC: 1553 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.83
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2827107; hg19: chr21-23254055;