rs225429

Variant names:

• chr21-42332376-G-A
• rs225429

Your query was ambiguous. Multiple possible variants found:

• chr21-42332376-G-A
• chr21-42332376-G-T

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 0.299 in 152,030 control chromosomes in the GnomAD database, including 8,764 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 0.30 (8764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 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: 0.299 AC: 45455 AN: 151912 Hom.: 8770 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.299 AC: 45451 AN: 152030 Hom.: 8764 Cov.: 32 AF XY: 0.295 AC XY: 21911 AN XY: 74308

African (AFR) AF: 0.0786 AC: 3262 AN: 41498

American (AMR) AF: 0.327 AC: 4995 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5178

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4810

European-Finnish (FIN) AF: 0.376 AC: 3968 AN: 10548

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28907 AN: 67924

Other (OTH) AF: 0.309 AC: 652 AN: 2110

Alfa AF: 0.238 Hom.: 687

Bravo AF: 0.285

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.38
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs225429; hg19: chr21-43752486;