chr3-100467401-A-G

Variant names:

• chr3-100467401-A-G
• rs9872227

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 0.774 in 152,052 control chromosomes in the GnomAD database, including 46,319 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 0.77 (46319 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.774 AC: 117571 AN: 151934 Hom.: 46249 Cov.: 30

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.774 AC: 117698 AN: 152052 Hom.: 46319 Cov.: 30 AF XY: 0.772 AC XY: 57419 AN XY: 74330

African (AFR) AF: 0.918 AC: 38088 AN: 41498

American (AMR) AF: 0.690 AC: 10538 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2623 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4723 AN: 5178

South Asian (SAS) AF: 0.704 AC: 3384 AN: 4810

European-Finnish (FIN) AF: 0.732 AC: 7728 AN: 10556

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48139 AN: 67958

Other (OTH) AF: 0.772 AC: 1633 AN: 2116

Alfa AF: 0.743 Hom.: 63129

Bravo AF: 0.781

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.14
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9872227; hg19: chr3-100186245;