9-104956027-A-G

Variant names:

• chr9-104956027-A-G
• rs2000068

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 0.397 in 151,026 control chromosomes in the GnomAD database, including 12,695 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 0.40 (12695 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.397 AC: 59904 AN: 150908 Hom.: 12683 Cov.: 29

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.397 AC: 59941 AN: 151026 Hom.: 12695 Cov.: 29 AF XY: 0.403 AC XY: 29697 AN XY: 73772

African (AFR) AF: 0.274 AC: 11247 AN: 41070

American (AMR) AF: 0.495 AC: 7511 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1629 AN: 3462

East Asian (EAS) AF: 0.672 AC: 3417 AN: 5082

South Asian (SAS) AF: 0.487 AC: 2326 AN: 4780

European-Finnish (FIN) AF: 0.470 AC: 4898 AN: 10422

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27441 AN: 67760

Other (OTH) AF: 0.417 AC: 868 AN: 2080

Alfa AF: 0.656 Hom.: 7262

Bravo AF: 0.399

Asia WGS AF: 0.542 AC: 1887 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	2.5
DANN	Benign	0.27
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2000068; hg19: chr9-107718308; COSMIC: COSV60387140;