rs9824873

Variant names:

• chr3-183583986-T-C
• rs9824873

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 0.34 in 152,140 control chromosomes in the GnomAD database, including 10,130 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 0.34 (10130 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.339 AC: 51582 AN: 152022 Hom.: 10103 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51665 AN: 152140 Hom.: 10130 Cov.: 33 AF XY: 0.338 AC XY: 25131 AN XY: 74388

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.340

Alfa AF: 0.254 Hom.: 10408

Bravo AF: 0.349

Asia WGS AF: 0.325 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9824873; hg19: chr3-183301774;