rs169482

Variant names:

• chr22-34409819-G-A
• rs169482

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 0.912 in 151,710 control chromosomes in the GnomAD database, including 63,162 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 0.91 (63162 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.912 AC: 138292 AN: 151614 Hom.: 63113 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.912 AC: 138389 AN: 151710 Hom.: 63162 Cov.: 31 AF XY: 0.917 AC XY: 67924 AN XY: 74104

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.903

Alfa AF: 0.904 Hom.: 8003

Bravo AF: 0.913

Asia WGS AF: 0.976 AC: 3374 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169482; hg19: chr22-34805809;