20-53733353-T-C

Position:

• chr20-53733353-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 0.274 in 151,866 control chromosomes in the GnomAD database, including 5,849 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 0.27 (5849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.274 AC: 41538 AN: 151748 Hom.: 5856 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.274 AC: 41541 AN: 151866 Hom.: 5849 Cov.: 32 AF XY: 0.274 AC XY: 20344 AN XY: 74214

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.276

Alfa AF: 0.284 Hom.: 12422

Bravo AF: 0.270

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6091737; hg19: chr20-52349892;