20-63223100-C-T

Position:

• chr20-63223100-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 0.154 in 152,146 control chromosomes in the GnomAD database, including 2,431 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 0.15 (2431 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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: 0.154 AC: 23349 AN: 152028 Hom.: 2420 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.154 AC: 23403 AN: 152146 Hom.: 2431 Cov.: 33 AF XY: 0.151 AC XY: 11219 AN XY: 74398

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0658

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.143

Alfa AF: 0.117 Hom.: 1385

Bravo AF: 0.163

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6011674; hg19: chr20-61854452;