6-33020918-T-G

Position:

• chr6-33020918-T-G

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 0.419 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.425

Alfa AF: 0.358 Hom.: 15333

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296068; hg19: chr6-32988695;