rs390208

Positions:

• chr16-84474211-G-A

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 0.156 in 151,974 control chromosomes in the GnomAD database, including 2,395 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 0.16 (2395 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23719 AN: 151866 Hom.: 2396 Cov.: 33

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.156 AC: 23717 AN: 151974 Hom.: 2395 Cov.: 33 AF XY: 0.162 AC XY: 12010 AN XY: 74260

Gnomad4 AFR AF: 0.0401

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.147

Alfa AF: 0.197 Hom.: 1563

Bravo AF: 0.143

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs390208; hg19: chr16-84507817;