chr7-22733108-G-A

Variant names:

• chr7-22733108-G-A
• rs1818879

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 0.306 in 152,010 control chromosomes in the GnomAD database, including 8,308 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 0.31 (8308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• Publications: 41 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 (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46499 AN: 151892 Hom.: 8303 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.306 AC: 46530 AN: 152010 Hom.: 8308 Cov.: 31 AF XY: 0.311 AC XY: 23133 AN XY: 74312

African (AFR) AF: 0.179 AC: 7424 AN: 41460

American (AMR) AF: 0.442 AC: 6747 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3466

East Asian (EAS) AF: 0.758 AC: 3921 AN: 5174

South Asian (SAS) AF: 0.439 AC: 2113 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2766 AN: 10544

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21883 AN: 67962

Other (OTH) AF: 0.309 AC: 650 AN: 2106

Alfa AF: 0.297 Hom.: 896

Bravo AF: 0.315

Asia WGS AF: 0.535 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1818879; hg19: chr7-22772727;