6-33053415-A-T

Position:

• chr6-33053415-A-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 0.798 in 152,064 control chromosomes in the GnomAD database, including 48,653 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 0.80 (48653 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33053415A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121196 AN: 151946 Hom.: 48616 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.798 AC: 121285 AN: 152064 Hom.: 48653 Cov.: 31 AF XY: 0.800 AC XY: 59444 AN XY: 74330

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.799

Alfa AF: 0.797 Hom.: 6051

Bravo AF: 0.782

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3128955; hg19: chr6-33021192;