20-53733353-T-C

Variant names:

• chr20-53733353-T-C
• rs6091737

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;