rs9860363

Variant names:

• chr3-166444785-T-C
• rs9860363

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 0.106 in 152,188 control chromosomes in the GnomAD database, including 1,107 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 0.11 (1107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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: 0.106 AC: 16165 AN: 152068 Hom.: 1097 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.106 AC: 16205 AN: 152188 Hom.: 1107 Cov.: 32 AF XY: 0.107 AC XY: 7973 AN XY: 74424

African (AFR) AF: 0.197 AC: 8178 AN: 41520

American (AMR) AF: 0.0522 AC: 798 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3470

East Asian (EAS) AF: 0.0789 AC: 405 AN: 5130

South Asian (SAS) AF: 0.0841 AC: 406 AN: 4830

European-Finnish (FIN) AF: 0.0994 AC: 1055 AN: 10618

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4806 AN: 68000

Other (OTH) AF: 0.0903 AC: 191 AN: 2116

Alfa AF: 0.100 Hom.: 100

Bravo AF: 0.105

Asia WGS AF: 0.0820 AC: 287 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.26
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9860363; hg19: chr3-166162573;