chr3-21266109-G-A

Variant names:

• chr3-21266109-G-A
• rs1344869

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 0.0811 in 152,066 control chromosomes in the GnomAD database, including 1,380 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 0.081 (1380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• 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 (AMR) allele frequency at 95% confidence interval = 0.311 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: 0.0809 AC: 12300 AN: 151948 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0811 AC: 12336 AN: 152066 Hom.: 1380 Cov.: 32 AF XY: 0.0871 AC XY: 6472 AN XY: 74342

African (AFR) AF: 0.0607 AC: 2520 AN: 41510

American (AMR) AF: 0.319 AC: 4865 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1280 AN: 5162

South Asian (SAS) AF: 0.161 AC: 777 AN: 4826

European-Finnish (FIN) AF: 0.0265 AC: 280 AN: 10568

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2198 AN: 67962

Other (OTH) AF: 0.0964 AC: 203 AN: 2106

Alfa AF: 0.0961 Hom.: 377

Bravo AF: 0.103

Asia WGS AF: 0.233 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.45
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1344869; hg19: chr3-21307601;