rs9347819

Variant names:

• chr6-164128680-C-T
• rs9347819

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 0.0728 in 152,158 control chromosomes in the GnomAD database, including 533 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 0.073 (533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0727 AC: 11050 AN: 152040 Hom.: 529 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0410

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0728 AC: 11083 AN: 152158 Hom.: 533 Cov.: 33 AF XY: 0.0757 AC XY: 5635 AN XY: 74394

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0410

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0494 Hom.: 473

Bravo AF: 0.0742

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9347819; hg19: chr6-164549712;