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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.554

Alfa AF: 0.610 Hom.: 31723

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701428; hg19: chr22-20228542;