chr20-53830764-A-G

Position:

• chr20-53830764-A-G

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 0.549 in 150,650 control chromosomes in the GnomAD database, including 23,136 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 0.55 (23136 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 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: 0.550 AC: 82724 AN: 150534 Hom.: 23129 Cov.: 29

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.549 AC: 82764 AN: 150650 Hom.: 23136 Cov.: 29 AF XY: 0.551 AC XY: 40432 AN XY: 73366

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.570

Alfa AF: 0.572 Hom.: 8980

Bravo AF: 0.549

Asia WGS AF: 0.511 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.014
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6022786; hg19: chr20-52447303;