rs9883654

Positions:

• chr3-153004186-C-T

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 0.475 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.449

Alfa AF: 0.428 Hom.: 31269

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9883654; hg19: chr3-152721975;