20-55215117-T-C

Position:

• chr20-55215117-T-C

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 0.172 in 152,158 control chromosomes in the GnomAD database, including 2,469 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 0.17 (2469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.172 AC: 26145 AN: 152040 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.172 AC: 26142 AN: 152158 Hom.: 2469 Cov.: 32 AF XY: 0.175 AC XY: 12993 AN XY: 74400

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.189

Alfa AF: 0.187 Hom.: 3637

Bravo AF: 0.165

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6092090; hg19: chr20-53831656;