rs9836282

Variant names:

• chr3-167024803-T-C
• rs9836282

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.456 AC: 18883 AN: 41406

American (AMR) AF: 0.521 AC: 7960 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1189 AN: 5168

South Asian (SAS) AF: 0.465 AC: 2237 AN: 4808

European-Finnish (FIN) AF: 0.389 AC: 4117 AN: 10582

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30218 AN: 67968

Other (OTH) AF: 0.440 AC: 928 AN: 2108

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs9836282; hg19: chr3-166742591;