rs9883474

Variant names:

• chr3-87476299-C-A
• rs9883474

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 0.163 in 152,096 control chromosomes in the GnomAD database, including 3,066 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 0.16 (3066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.163 AC: 24751 AN: 151978 Hom.: 3056 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.163 AC: 24788 AN: 152096 Hom.: 3066 Cov.: 32 AF XY: 0.164 AC XY: 12216 AN XY: 74356

African (AFR) AF: 0.354 AC: 14657 AN: 41458

American (AMR) AF: 0.0836 AC: 1276 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.0873 AC: 452 AN: 5176

South Asian (SAS) AF: 0.0930 AC: 449 AN: 4830

European-Finnish (FIN) AF: 0.161 AC: 1702 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0813 AC: 5527 AN: 67994

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.104 Hom.: 3934

Bravo AF: 0.166

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.83
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9883474; hg19: chr3-87525449;