rs16999165

chr20-54190682-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 0.0577 in 152,292 control chromosomes in the GnomAD database, including 469 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 0.058 (469 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.0576 AC: 8766 AN: 152174 Hom.: 465 Cov.: 34

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0577 AC: 8785 AN: 152292 Hom.: 469 Cov.: 34 AF XY: 0.0596 AC XY: 4436 AN XY: 74468

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0424 Hom.: 139

Bravo AF: 0.0624

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16999165; hg19: chr20-52807221;