20-53652456-T-G

Variant names:

• chr20-53652456-T-G
• rs2041278

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 0.565 in 152,020 control chromosomes in the GnomAD database, including 26,242 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 0.57 (26242 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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: 0.566 AC: 85938 AN: 151902 Hom.: 26246 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.565 AC: 85946 AN: 152020 Hom.: 26242 Cov.: 33 AF XY: 0.568 AC XY: 42215 AN XY: 74324

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.579

Alfa AF: 0.649 Hom.: 67859

Bravo AF: 0.543

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	17
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2041278; hg19: chr20-52268995;