16-84470981-C-T

Variant names:

• chr16-84470981-C-T
• rs394533

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 0.308 in 151,534 control chromosomes in the GnomAD database, including 7,696 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 0.31 (7696 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.433 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: 0.308 AC: 46615 AN: 151416 Hom.: 7670 Cov.: 30

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.308 AC: 46688 AN: 151534 Hom.: 7696 Cov.: 30 AF XY: 0.313 AC XY: 23137 AN XY: 74000

African (AFR) AF: 0.419 AC: 17298 AN: 41262

American (AMR) AF: 0.276 AC: 4207 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1083 AN: 3460

East Asian (EAS) AF: 0.212 AC: 1089 AN: 5128

South Asian (SAS) AF: 0.449 AC: 2161 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3238 AN: 10438

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16679 AN: 67902

Other (OTH) AF: 0.281 AC: 592 AN: 2106

Alfa AF: 0.268 Hom.: 11203

Bravo AF: 0.305

Asia WGS AF: 0.328 AC: 1138 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	7.0
DANN	Benign	0.82
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs394533; hg19: chr16-84504587;