rs9354792

chr6-68597003-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 0.578 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/exons	MANE	UniProt

Ensembl

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