rs16999165

Variant names:

• chr20-54190682-A-G
• rs16999165

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;