rs1569428

Variant names:

• chr22-34394136-A-G
• rs1569428

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 0.355 in 152,048 control chromosomes in the GnomAD database, including 10,310 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 0.36 (10310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 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: 0.355 AC: 53985 AN: 151930 Hom.: 10309 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.355 AC: 53992 AN: 152048 Hom.: 10310 Cov.: 32 AF XY: 0.352 AC XY: 26181 AN XY: 74326

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.344

Alfa AF: 0.379 Hom.: 1929

Bravo AF: 0.338

Asia WGS AF: 0.251 AC: 875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569428; hg19: chr22-34790126;