rs9354792

Variant names:

• chr6-68597003-G-A
• rs9354792

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 0.578 in 151,970 control chromosomes in the GnomAD database, including 26,065 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 0.58 (26065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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 = 0.707 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: 0.578 AC: 87696 AN: 151852 Hom.: 26020 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.578 AC: 87800 AN: 151970 Hom.: 26065 Cov.: 31 AF XY: 0.577 AC XY: 42845 AN XY: 74260

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.514

Alfa AF: 0.569 Hom.: 4228

Bravo AF: 0.578

Asia WGS AF: 0.484 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9354792; hg19: chr6-69306895;