rs701428

Variant names:

• chr22-20241019-A-G
• rs701428

Your query was ambiguous. Multiple possible variants found:

• chr22-20241019-A-G
• chr22-20241019-A-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 0.559 in 151,972 control chromosomes in the GnomAD database, including 24,494 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 0.56 (24494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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: 0.559 AC: 84932 AN: 151854 Hom.: 24495 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.559 AC: 84952 AN: 151972 Hom.: 24494 Cov.: 33 AF XY: 0.558 AC XY: 41470 AN XY: 74280

African (AFR) AF: 0.430 AC: 17832 AN: 41438

American (AMR) AF: 0.505 AC: 7727 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2161 AN: 3472

East Asian (EAS) AF: 0.584 AC: 2996 AN: 5130

South Asian (SAS) AF: 0.528 AC: 2542 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7144 AN: 10592

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42801 AN: 67920

Other (OTH) AF: 0.554 AC: 1172 AN: 2114

Alfa AF: 0.589 Hom.: 46699

Bravo AF: 0.539

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.70
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs701428; hg19: chr22-20228542;