chr3-22699973-A-G

Variant names:

• chr3-22699973-A-G
• rs11129085

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 0.598 in 151,840 control chromosomes in the GnomAD database, including 27,606 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 0.60 (27606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90807 AN: 151722 Hom.: 27597 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.598 AC: 90857 AN: 151840 Hom.: 27606 Cov.: 32 AF XY: 0.598 AC XY: 44397 AN XY: 74228

African (AFR) AF: 0.652 AC: 27047 AN: 41510

American (AMR) AF: 0.668 AC: 10189 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1799 AN: 3456

East Asian (EAS) AF: 0.674 AC: 3483 AN: 5164

South Asian (SAS) AF: 0.681 AC: 3283 AN: 4822

European-Finnish (FIN) AF: 0.444 AC: 4689 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38359 AN: 67758

Other (OTH) AF: 0.599 AC: 1266 AN: 2112

Alfa AF: 0.575 Hom.: 14858

Bravo AF: 0.616

Asia WGS AF: 0.668 AC: 2318 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.79
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11129085; hg19: chr3-22741464;