rs11466306

Variant names:

• chr2-70447020-C-T
• rs11466306

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 0.224 in 152,162 control chromosomes in the GnomAD database, including 4,300 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 0.22 (4300 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.224 AC: 34049 AN: 152044 Hom.: 4292 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.224 AC: 34061 AN: 152162 Hom.: 4300 Cov.: 33 AF XY: 0.224 AC XY: 16681 AN XY: 74376

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.224

Alfa AF: 0.244 Hom.: 1279

Bravo AF: 0.208

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11466306; hg19: chr2-70674152;