rs9325634

Positions:

• chr21-42398681-A-G
• chr21-42398681-A-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 0.43 in 151,998 control chromosomes in the GnomAD database, including 14,248 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 0.43 (14248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.430 AC: 65267 AN: 151880 Hom.: 14241 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.430 AC: 65298 AN: 151998 Hom.: 14248 Cov.: 32 AF XY: 0.424 AC XY: 31457 AN XY: 74272

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.433

Alfa AF: 0.455 Hom.: 7671

Bravo AF: 0.424

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9325634; hg19: chr21-43818790;