chr9-133278724-C-T

Variant names:

• chr9-133278724-C-T
• rs579459

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 152,126 control chromosomes in the GnomAD database, including 50,002 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 (50002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 257 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122932 AN: 152008 Hom.: 49938 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.809 AC: 123054 AN: 152126 Hom.: 50002 Cov.: 32 AF XY: 0.812 AC XY: 60382 AN XY: 74370

African (AFR) AF: 0.862 AC: 35740 AN: 41470

American (AMR) AF: 0.829 AC: 12682 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4124 AN: 5182

South Asian (SAS) AF: 0.840 AC: 4049 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8204 AN: 10580

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

European-Non Finnish (NFE) AF: 0.781 AC: 53131 AN: 67994

Other (OTH) AF: 0.806 AC: 1700 AN: 2110

Alfa AF: 0.787 Hom.: 189258

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs579459; hg19: chr9-136154168;