20-39061821-A-G

Variant names:

• chr20-39061821-A-G
• rs926392

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 0.53 in 151,922 control chromosomes in the GnomAD database, including 22,244 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 0.53 (22244 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.530 AC: 80430 AN: 151804 Hom.: 22203 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.530 AC: 80531 AN: 151922 Hom.: 22244 Cov.: 31 AF XY: 0.529 AC XY: 39310 AN XY: 74248

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.532

Alfa AF: 0.452 Hom.: 18122

Bravo AF: 0.552

Asia WGS AF: 0.608 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926392; hg19: chr20-37690464;