chr16-84474211-G-A

Variant names:

• chr16-84474211-G-A
• rs390208

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 0.156 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0401 AC: 1661 AN: 41434

American (AMR) AF: 0.181 AC: 2767 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3468

East Asian (EAS) AF: 0.0456 AC: 236 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4810

European-Finnish (FIN) AF: 0.275 AC: 2897 AN: 10522

Middle Eastern (MID) AF: 0.197 AC: 57 AN: 290

European-Non Finnish (NFE) AF: 0.204 AC: 13885 AN: 67982

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.191 Hom.: 2135

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
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs390208; hg19: chr16-84507817;