rs16988591

chr20-39914800-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;