rs9824873

chr3-183583986-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;