rs9883805

Variant names:

• chr3-110242347-A-G
• rs9883805

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 152,146 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
• Publications: 2 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.289 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: 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

African (AFR) AF: 0.293 AC: 12159 AN: 41466

American (AMR) AF: 0.149 AC: 2276 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1297 AN: 5142

South Asian (SAS) AF: 0.0977 AC: 471 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1083 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6777 AN: 68022

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.130 Hom.: 1071

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs9883805; hg19: chr3-109961194;