chr6-33111389-C-T

Variant names:

• chr6-33111389-C-T
• rs9380343

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 0.0523 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
• Publications: 36 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0460 AC: 1905 AN: 41442

American (AMR) AF: 0.0395 AC: 603 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0445 AC: 154 AN: 3464

East Asian (EAS) AF: 0.424 AC: 2190 AN: 5168

South Asian (SAS) AF: 0.0246 AC: 118 AN: 4788

European-Finnish (FIN) AF: 0.0323 AC: 342 AN: 10578

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0365 AC: 2483 AN: 67942

Other (OTH) AF: 0.0627 AC: 132 AN: 2106

Alfa AF: 0.0467 Hom.: 1810

Bravo AF: 0.0542

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.50
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs9380343; hg19: chr6-33079166;