20-6357333-C-T

Position:

• chr20-6357333-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 0.708 in 152,096 control chromosomes in the GnomAD database, including 38,880 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 0.71 (38880 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6357333C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107537 AN: 151978 Hom.: 38840 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.708 AC: 107638 AN: 152096 Hom.: 38880 Cov.: 33 AF XY: 0.707 AC XY: 52566 AN XY: 74364

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.748

Alfa AF: 0.656 Hom.: 21791

Bravo AF: 0.726

Asia WGS AF: 0.738 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.059
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038449; hg19: chr20-6337980;