3-186870467-A-G

Variant names:

• chr3-186870467-A-G
• rs1501296

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 0.331 in 152,080 control chromosomes in the GnomAD database, including 9,273 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 0.33 (9273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50260 AN: 151964 Hom.: 9246 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.331 AC: 50336 AN: 152080 Hom.: 9273 Cov.: 32 AF XY: 0.330 AC XY: 24560 AN XY: 74356

African (AFR) AF: 0.486 AC: 20122 AN: 41442

American (AMR) AF: 0.316 AC: 4832 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1218 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2397 AN: 5178

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2475 AN: 10592

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16630 AN: 67990

Other (OTH) AF: 0.350 AC: 738 AN: 2108

Alfa AF: 0.271 Hom.: 3334

Bravo AF: 0.343

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1501296; hg19: chr3-186588256;