rs9836282

Positions:

• chr3-167024803-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 0.446 in 151,978 control chromosomes in the GnomAD database, including 15,353 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 0.45 (15353 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67756 AN: 151860 Hom.: 15340 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.446 AC: 67807 AN: 151978 Hom.: 15353 Cov.: 32 AF XY: 0.446 AC XY: 33114 AN XY: 74288

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.440

Alfa AF: 0.468 Hom.: 2794

Bravo AF: 0.451

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.082
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9836282; hg19: chr3-166742591;