rs9809107

chr3-44241442-G-A

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 0.473 in 152,108 control chromosomes in the GnomAD database, including 17,906 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 0.47 (17906 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.473 AC: 71929 AN: 151990 Hom.: 17890 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.473 AC: 71987 AN: 152108 Hom.: 17906 Cov.: 33 AF XY: 0.481 AC XY: 35796 AN XY: 74370

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.467

Alfa AF: 0.485 Hom.: 28702

Bravo AF: 0.471

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.8
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9809107; hg19: chr3-44282934;