rs16999397

chr20-243487-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 0.344 in 151,940 control chromosomes in the GnomAD database, including 10,099 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 0.34 (10099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 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: 0.345 AC: 52308 AN: 151822 Hom.: 10100 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.344 AC: 52315 AN: 151940 Hom.: 10099 Cov.: 32 AF XY: 0.348 AC XY: 25822 AN XY: 74226

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.341

Alfa AF: 0.404 Hom.: 16526

Bravo AF: 0.339

Asia WGS AF: 0.287 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.73
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16999397; hg19: chr20-224128;