rs9872227

Variant names:

• chr3-100467401-A-G
• rs9872227

Your query was ambiguous. Multiple possible variants found:

• chr3-100467401-A-G
• chr3-100467401-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.774 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

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.772

Alfa AF: 0.750 Hom.: 7284

Bravo AF: 0.781

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9872227; hg19: chr3-100186245;