16-84953108-G-T

Variant names:

• chr16-84953108-G-T
• rs8061778

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 0.261 in 152,126 control chromosomes in the GnomAD database, including 5,958 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 0.26 (5958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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: 0.260 AC: 39572 AN: 152008 Hom.: 5935 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.261 AC: 39647 AN: 152126 Hom.: 5958 Cov.: 32 AF XY: 0.256 AC XY: 19081 AN XY: 74398

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.242

Alfa AF: 0.196 Hom.: 2924

Bravo AF: 0.270

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8061778; hg19: chr16-84986714;