chr6-33020918-T-G

Variant names:

• chr6-33020918-T-G
• rs9296068

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 0.419 in 152,092 control chromosomes in the GnomAD database, including 14,026 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 0.42 (14026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 47 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 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: 0.419 AC: 63680 AN: 151974 Hom.: 14012 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.419 AC: 63723 AN: 152092 Hom.: 14026 Cov.: 32 AF XY: 0.425 AC XY: 31578 AN XY: 74370

African (AFR) AF: 0.539 AC: 22348 AN: 41476

American (AMR) AF: 0.373 AC: 5697 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1808 AN: 3466

East Asian (EAS) AF: 0.469 AC: 2426 AN: 5176

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4818

European-Finnish (FIN) AF: 0.465 AC: 4912 AN: 10562

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23160 AN: 67990

Other (OTH) AF: 0.425 AC: 900 AN: 2116

Alfa AF: 0.363 Hom.: 40872

Bravo AF: 0.415

Asia WGS AF: 0.489 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.41
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9296068; hg19: chr6-32988695;