rs16999165

Variant names:

• chr20-54190682-A-G
• rs16999165

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0677 AC: 2815 AN: 41560

American (AMR) AF: 0.0661 AC: 1011 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5180

South Asian (SAS) AF: 0.0683 AC: 330 AN: 4830

European-Finnish (FIN) AF: 0.0360 AC: 382 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2366 AN: 68032

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0467 Hom.: 630

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs16999165; hg19: chr20-52807221;