rs294222

Variant names:

• chr1-22681067-C-G
• rs294222

Your query was ambiguous. Multiple possible variants found:

• chr1-22681067-C-G
• chr1-22681067-C-T

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 0.761 in 152,138 control chromosomes in the GnomAD database, including 44,377 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 0.76 (44377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.761 AC: 115689 AN: 152020 Hom.: 44330 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.761 AC: 115787 AN: 152138 Hom.: 44377 Cov.: 32 AF XY: 0.757 AC XY: 56267 AN XY: 74350

African (AFR) AF: 0.860 AC: 35713 AN: 41512

American (AMR) AF: 0.756 AC: 11551 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3138 AN: 5164

South Asian (SAS) AF: 0.717 AC: 3456 AN: 4820

European-Finnish (FIN) AF: 0.669 AC: 7069 AN: 10568

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49742 AN: 68010

Other (OTH) AF: 0.761 AC: 1605 AN: 2110

Alfa AF: 0.675 Hom.: 2193

Bravo AF: 0.772

Asia WGS AF: 0.708 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs294222; hg19: chr1-23007560;