chr3-22667311-T-C

Variant names:

• chr3-22667311-T-C
• rs1466352

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 0.614 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.615 AC: 25502 AN: 41490

American (AMR) AF: 0.623 AC: 9522 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3149 AN: 5174

South Asian (SAS) AF: 0.676 AC: 3258 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5862 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42182 AN: 67982

Other (OTH) AF: 0.605 AC: 1280 AN: 2114

Alfa AF: 0.616 Hom.: 14198

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1466352; hg19: chr3-22708802;