20-54125940-T-A

Position:

• chr20-54125940-T-A

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 0.233 in 152,124 control chromosomes in the GnomAD database, including 4,269 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 0.23 (4269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35370 AN: 152006 Hom.: 4256 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.233 AC: 35430 AN: 152124 Hom.: 4269 Cov.: 32 AF XY: 0.234 AC XY: 17402 AN XY: 74376

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.239

Alfa AF: 0.109 Hom.: 164

Bravo AF: 0.240

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6013897; hg19: chr20-52742479;