rs1466352

chr3-22667311-T-C

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 0.614 in 152,108 control chromosomes in the GnomAD database, including 28,801 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 0.61 (28801 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93349 AN: 151990 Hom.: 28800 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.614 AC: 93389 AN: 152108 Hom.: 28801 Cov.: 33 AF XY: 0.613 AC XY: 45576 AN XY: 74344

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.605

Alfa AF: 0.616 Hom.: 12593

Bravo AF: 0.617

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.17
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466352; hg19: chr3-22708802;