rs66800491

Variant names:

• chr3-109915280-G-A
• rs66800491

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 0.286 in 150,966 control chromosomes in the GnomAD database, including 6,419 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 0.29 (6419 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43146 AN: 150854 Hom.: 6408 Cov.: 29

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.286 AC: 43174 AN: 150966 Hom.: 6419 Cov.: 29 AF XY: 0.290 AC XY: 21366 AN XY: 73628

African (AFR) AF: 0.209 AC: 8596 AN: 41092

American (AMR) AF: 0.242 AC: 3674 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1542 AN: 5108

South Asian (SAS) AF: 0.438 AC: 2089 AN: 4772

European-Finnish (FIN) AF: 0.309 AC: 3156 AN: 10220

Middle Eastern (MID) AF: 0.295 AC: 85 AN: 288

European-Non Finnish (NFE) AF: 0.324 AC: 21981 AN: 67820

Other (OTH) AF: 0.299 AC: 629 AN: 2102

Alfa AF: 0.309 Hom.: 9836

Bravo AF: 0.272

Asia WGS AF: 0.352 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.60
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs66800491; hg19: chr3-109634127;