20-6357333-C-T

Variant names:

• chr20-6357333-C-T
• rs6038449

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;