20-6054582-C-T

Position:

• chr20-6054582-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 0.771 in 151,866 control chromosomes in the GnomAD database, including 45,598 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 0.77 (45598 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117052 AN: 151750 Hom.: 45552 Cov.: 30

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.771 AC: 117157 AN: 151866 Hom.: 45598 Cov.: 30 AF XY: 0.768 AC XY: 57016 AN XY: 74202

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.785

Alfa AF: 0.739 Hom.: 91830

Bravo AF: 0.786

Asia WGS AF: 0.817 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326679; hg19: chr20-6035228;