9-133279294-T-G

Variant names:

• chr9-133279294-T-G
• rs495828

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 0.809 in 152,092 control chromosomes in the GnomAD database, including 50,070 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 0.81 (50070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 164 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122993 AN: 151974 Hom.: 50005 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.809 AC: 123116 AN: 152092 Hom.: 50070 Cov.: 31 AF XY: 0.812 AC XY: 60402 AN XY: 74350

African (AFR) AF: 0.864 AC: 35818 AN: 41480

American (AMR) AF: 0.830 AC: 12675 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4124 AN: 5160

South Asian (SAS) AF: 0.839 AC: 4043 AN: 4816

European-Finnish (FIN) AF: 0.775 AC: 8191 AN: 10572

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

European-Non Finnish (NFE) AF: 0.781 AC: 53139 AN: 68002

Other (OTH) AF: 0.805 AC: 1702 AN: 2114

Alfa AF: 0.801 Hom.: 7918

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs495828; hg19: chr9-136154867;