rs9380343

Positions:

• chr6-33111389-C-T

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/exons	MANE	UniProt

Ensembl

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