6-33234863-C-T

Position:

• chr6-33234863-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 0.584 in 151,872 control chromosomes in the GnomAD database, including 26,512 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 0.58 (26512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.584 AC: 88643 AN: 151754 Hom.: 26493 Cov.: 30

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.584 AC: 88701 AN: 151872 Hom.: 26512 Cov.: 30 AF XY: 0.581 AC XY: 43087 AN XY: 74176

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.652

Alfa AF: 0.551 Hom.: 32342

Bravo AF: 0.594

Asia WGS AF: 0.716 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs213220; hg19: chr6-33202640;