rs9380343

Variant names:

• chr6-33111389-C-T
• rs9380343

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 0.0523 in 151,970 control chromosomes in the GnomAD database, including 617 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 0.052 (617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 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: 0.0522 AC: 7925 AN: 151852 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0528

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

GnomAD4 genome AF: 0.0523 AC: 7951 AN: 151970 Hom.: 617 Cov.: 32 AF XY: 0.0532 AC XY: 3949 AN XY: 74294

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.0323

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0469 Hom.: 881

Bravo AF: 0.0542

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380343; hg19: chr6-33079166;