20-1724828-C-T

Position:

• chr20-1724828-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 0.375 in 151,916 control chromosomes in the GnomAD database, including 11,346 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 0.37 (11346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 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: 0.374 AC: 56849 AN: 151800 Hom.: 11334 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.375 AC: 56898 AN: 151916 Hom.: 11346 Cov.: 32 AF XY: 0.371 AC XY: 27587 AN XY: 74262

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.360

Alfa AF: 0.390 Hom.: 3453

Bravo AF: 0.376

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202518; hg19: chr20-1705474;