rs16988591

Variant names:

• chr20-39914800-T-C
• rs16988591

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 0.216 in 151,992 control chromosomes in the GnomAD database, including 4,056 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 0.22 (4056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 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: 0.216 AC: 32798 AN: 151874 Hom.: 4056 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.216 AC: 32808 AN: 151992 Hom.: 4056 Cov.: 32 AF XY: 0.220 AC XY: 16336 AN XY: 74290

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.184

Alfa AF: 0.247 Hom.: 7522

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16988591; hg19: chr20-38543442;