16-84470981-C-T

Variant names:

• chr16-84470981-C-T
• rs394533

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 0.308 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.308 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

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.281

Alfa AF: 0.258 Hom.: 3045

Bravo AF: 0.305

Asia WGS AF: 0.328 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs394533; hg19: chr16-84504587;