rs16989303

chr20-4188432-G-A

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 0.0357 in 152,148 control chromosomes in the GnomAD database, including 184 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 0.036 (184 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0357 AC: 5435 AN: 152030 Hom.: 185 Cov.: 31

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0357 AC: 5432 AN: 152148 Hom.: 184 Cov.: 31 AF XY: 0.0356 AC XY: 2651 AN XY: 74406

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0237

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0453 Hom.: 284

Bravo AF: 0.0369

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	13
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16989303; hg19: chr20-4169079;