3-161979301-A-G

Variant names:

• chr3-161979301-A-G
• rs9812882

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 0.226 in 152,042 control chromosomes in the GnomAD database, including 4,050 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 0.23 (4050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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: 0.226 AC: 34385 AN: 151924 Hom.: 4036 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.226 AC: 34424 AN: 152042 Hom.: 4050 Cov.: 33 AF XY: 0.230 AC XY: 17071 AN XY: 74288

African (AFR) AF: 0.211 AC: 8753 AN: 41480

American (AMR) AF: 0.188 AC: 2872 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2167 AN: 5142

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4814

European-Finnish (FIN) AF: 0.304 AC: 3212 AN: 10562

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14839 AN: 67966

Other (OTH) AF: 0.223 AC: 470 AN: 2110

Alfa AF: 0.214 Hom.: 577

Bravo AF: 0.214

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Publications

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Other links and lift over

dbSNP: rs9812882; hg19: chr3-161697089;