rs169482

Variant names:

• chr22-34409819-G-A
• rs169482

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 0.912 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.925 AC: 38360 AN: 41468

American (AMR) AF: 0.936 AC: 14240 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3196 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5164 AN: 5166

South Asian (SAS) AF: 0.976 AC: 4702 AN: 4816

European-Finnish (FIN) AF: 0.919 AC: 9546 AN: 10384

Middle Eastern (MID) AF: 0.931 AC: 270 AN: 290

European-Non Finnish (NFE) AF: 0.886 AC: 60145 AN: 67886

Other (OTH) AF: 0.903 AC: 1902 AN: 2106

Alfa AF: 0.905 Hom.: 8558

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
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs169482; hg19: chr22-34805809;