rs579459

Variant names:

• chr9-133278724-C-T
• rs579459

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 0.809 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.806

Alfa AF: 0.779 Hom.: 73401

Bravo AF: 0.813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs579459; hg19: chr9-136154168;