rs66800491

Variant names:

• chr3-109915280-G-A
• rs66800491

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.286 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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.299

Alfa AF: 0.311 Hom.: 916

Bravo AF: 0.272

Asia WGS AF: 0.352 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs66800491; hg19: chr3-109634127;