rs16999397

Variant names:

• chr20-243487-T-C
• rs16999397

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 0.344 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.158 AC: 6558 AN: 41462

American (AMR) AF: 0.449 AC: 6841 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1593 AN: 5178

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4806

European-Finnish (FIN) AF: 0.390 AC: 4106 AN: 10526

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28446 AN: 67932

Other (OTH) AF: 0.341 AC: 721 AN: 2112

Alfa AF: 0.402 Hom.: 19318

Bravo AF: 0.339

Asia WGS AF: 0.287 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs16999397; hg19: chr20-224128;