rs9615812

Variant names:

• chr22-48221836-G-A
• rs9615812

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 0.0928 in 152,158 control chromosomes in the GnomAD database, including 726 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 0.093 (726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0929 AC: 14123 AN: 152040 Hom.: 728 Cov.: 33

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0928 AC: 14118 AN: 152158 Hom.: 726 Cov.: 33 AF XY: 0.0893 AC XY: 6642 AN XY: 74380

African (AFR) AF: 0.0963 AC: 3996 AN: 41514

American (AMR) AF: 0.0544 AC: 831 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0615 AC: 213 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4812

European-Finnish (FIN) AF: 0.144 AC: 1520 AN: 10590

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7187 AN: 67986

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0992 Hom.: 133

Bravo AF: 0.0873

Asia WGS AF: 0.0170 AC: 58 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.088
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9615812; hg19: chr22-48617648;