rs9872227

chr3-100467401-A-Gchr3-100467401-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;