rs9829637

chr3-134437220-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 0.331 in 152,162 control chromosomes in the GnomAD database, including 8,719 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 0.33 (8719 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.331 AC: 50298 AN: 152044 Hom.: 8699 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.331 AC: 50348 AN: 152162 Hom.: 8719 Cov.: 33 AF XY: 0.326 AC XY: 24251 AN XY: 74390

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0906

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.330

Alfa AF: 0.359 Hom.: 1244

Bravo AF: 0.332

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9829637; hg19: chr3-134156062;