rs17283813

Variant names:

• chr3-188921906-G-A
• rs17283813

Your query was ambiguous. Multiple possible variants found:

• chr3-188921906-G-A
• chr3-188921906-G-T

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 0.0803 in 152,204 control chromosomes in the GnomAD database, including 657 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 0.080 (657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 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: 0.0803 AC: 12220 AN: 152086 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0803 AC: 12222 AN: 152204 Hom.: 657 Cov.: 32 AF XY: 0.0788 AC XY: 5867 AN XY: 74426

African (AFR) AF: 0.0215 AC: 893 AN: 41542

American (AMR) AF: 0.0820 AC: 1252 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4830

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8151 AN: 67994

Other (OTH) AF: 0.0851 AC: 180 AN: 2116

Alfa AF: 0.0915 Hom.: 942

Bravo AF: 0.0739

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.60
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs17283813; hg19: chr3-188639695;