rs9321063

Variant names:

• chr6-98448791-A-G
• rs9321063

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 0.0695 in 152,172 control chromosomes in the GnomAD database, including 413 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 0.069 (413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 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: 0.0694 AC: 10548 AN: 152054 Hom.: 412 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00737

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0695 AC: 10569 AN: 152172 Hom.: 413 Cov.: 33 AF XY: 0.0705 AC XY: 5243 AN XY: 74372

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00719

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0586 Hom.: 366

Bravo AF: 0.0717

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321063; hg19: chr6-98896667;