rs579459

chr9-133278724-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;