rs9883654

Variant names:

• chr3-153004186-C-T
• rs9883654

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 0.475 in 152,050 control chromosomes in the GnomAD database, including 17,791 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 0.48 (17791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.475 AC: 72153 AN: 151932 Hom.: 17754 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.475 AC: 72252 AN: 152050 Hom.: 17791 Cov.: 32 AF XY: 0.478 AC XY: 35562 AN XY: 74324

African (AFR) AF: 0.592 AC: 24553 AN: 41472

American (AMR) AF: 0.462 AC: 7056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2429 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4816

European-Finnish (FIN) AF: 0.457 AC: 4833 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28367 AN: 67948

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.436 Hom.: 66739

Bravo AF: 0.481

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.35
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9883654; hg19: chr3-152721975;