6-33510719-A-G

Variant names:

• chr6-33510719-A-G
• rs9296092

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 0.558 in 152,126 control chromosomes in the GnomAD database, including 26,849 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 0.56 (26849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.558 AC: 84884 AN: 152008 Hom.: 26848 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.558 AC: 84906 AN: 152126 Hom.: 26849 Cov.: 33 AF XY: 0.573 AC XY: 42585 AN XY: 74360

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.587

Alfa AF: 0.639 Hom.: 57155

Bravo AF: 0.528

Asia WGS AF: 0.825 AC: 2868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296092; hg19: chr6-33478496;