6-52803889-A-G

Position:

• chr6-52803889-A-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 0.623 in 211,512 control chromosomes in the GnomAD database, including 41,992 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 0.63 (30760 hom., cov: 32)
  • Exomes 𝑓: 0.60 (11232 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52803889A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTA1	ENST00000476213.1	n.-29T>C		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95666 AN: 151806 Hom.: 30741 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.627

GnomAD4 exome AF: 0.603 AC: 35950 AN: 59590 Hom.: 11232 Cov.: 0 AF XY: 0.599 AC XY: 16551 AN XY: 27618

Gnomad4 AFR exome AF: 0.651

Gnomad4 AMR exome AF: 0.688

Gnomad4 ASJ exome AF: 0.526

Gnomad4 EAS exome AF: 0.866

Gnomad4 SAS exome AF: 0.661

Gnomad4 FIN exome AF: 0.522

Gnomad4 NFE exome AF: 0.544

Gnomad4 OTH exome AF: 0.579

GnomAD4 genome AF: 0.630 AC: 95732 AN: 151922 Hom.: 30760 Cov.: 32 AF XY: 0.633 AC XY: 47024 AN XY: 74252

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.631

Alfa AF: 0.616 Hom.: 3546

Bravo AF: 0.643

Asia WGS AF: 0.737 AC: 2560 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3957357; hg19: chr6-52668687;