rs16989303

Variant names:

• chr20-4188432-G-A
• rs16989303

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 0.0357 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0115 AC: 477 AN: 41520

American (AMR) AF: 0.0364 AC: 556 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.186 AC: 960 AN: 5152

South Asian (SAS) AF: 0.0237 AC: 114 AN: 4820

European-Finnish (FIN) AF: 0.0313 AC: 332 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2883 AN: 67984

Other (OTH) AF: 0.0242 AC: 51 AN: 2108

Alfa AF: 0.0431 Hom.: 576

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs16989303; hg19: chr20-4169079;