chr16-20082732-A-G

Position:

• chr16-20082732-A-G

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 0.25 in 151,826 control chromosomes in the GnomAD database, including 4,798 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 0.25 (4798 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.250 AC: 37984 AN: 151708 Hom.: 4798 Cov.: 30

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.250 AC: 38020 AN: 151826 Hom.: 4798 Cov.: 30 AF XY: 0.252 AC XY: 18701 AN XY: 74176

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.231

Alfa AF: 0.258 Hom.: 945

Bravo AF: 0.249

Asia WGS AF: 0.243 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7201408; hg19: chr16-20094054;