20-56252715-T-A

Position:

• chr20-56252715-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 0.078 in 152,162 control chromosomes in the GnomAD database, including 591 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 0.078 (591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 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: 0.0779 AC: 11851 AN: 152044 Hom.: 593 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0780 AC: 11866 AN: 152162 Hom.: 591 Cov.: 32 AF XY: 0.0815 AC XY: 6063 AN XY: 74400

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0606 Hom.: 46

Bravo AF: 0.0764

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6123569; hg19: chr20-54827771;