rs9883805

chr3-110242347-A-G

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 0.163 in 152,146 control chromosomes in the GnomAD database, including 2,584 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 (2584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.163 AC: 24727 AN: 152026 Hom.: 2576 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.163 AC: 24760 AN: 152146 Hom.: 2584 Cov.: 32 AF XY: 0.161 AC XY: 12006 AN XY: 74404

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.147

Alfa AF: 0.128 Hom.: 919

Bravo AF: 0.174

Asia WGS AF: 0.190 AC: 660 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	4.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9883805; hg19: chr3-109961194;