rs9393529

Variant names:

• chr6-24124481-G-A
• rs9393529

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 0.0717 in 152,094 control chromosomes in the GnomAD database, including 537 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 0.072 (537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.0718 AC: 10906 AN: 151976 Hom.: 539 Cov.: 33

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0717 AC: 10899 AN: 152094 Hom.: 537 Cov.: 33 AF XY: 0.0755 AC XY: 5615 AN XY: 74332

Gnomad4 AFR AF: 0.0161

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0703 Hom.: 57

Bravo AF: 0.0654

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9393529; hg19: chr6-24124709;