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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.299 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

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.309

Alfa AF: 0.248 Hom.: 682

Bravo AF: 0.285

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225429; hg19: chr21-43752486;