rs9354792

Variant names:

• chr6-68597003-G-A
• rs9354792

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.714 AC: 29601 AN: 41466

American (AMR) AF: 0.549 AC: 8382 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1475 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1798 AN: 5144

South Asian (SAS) AF: 0.571 AC: 2754 AN: 4820

European-Finnish (FIN) AF: 0.586 AC: 6185 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36079 AN: 67942

Other (OTH) AF: 0.514 AC: 1085 AN: 2112

Alfa AF: 0.573 Hom.: 4425

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9354792; hg19: chr6-69306895;