rs9393529

chr6-24124481-G-A

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/exons	MANE	UniProt

Ensembl

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