20-6858477-C-T

Position:

• chr20-6858477-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 0.591 in 151,946 control chromosomes in the GnomAD database, including 28,101 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 0.59 (28101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89691 AN: 151824 Hom.: 28047 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.591 AC: 89811 AN: 151946 Hom.: 28101 Cov.: 31 AF XY: 0.588 AC XY: 43637 AN XY: 74258

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.579

Alfa AF: 0.397 Hom.: 1077

Bravo AF: 0.609

Asia WGS AF: 0.651 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1500537; hg19: chr20-6839124;