16-8453220-G-A

Position:

• chr16-8453220-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.851 in 152,212 control chromosomes in the GnomAD database, including 55,374 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 0.85 (55374 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129388 AN: 152094 Hom.: 55332 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.851 AC: 129482 AN: 152212 Hom.: 55374 Cov.: 33 AF XY: 0.853 AC XY: 63480 AN XY: 74394

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.844

Alfa AF: 0.842 Hom.: 10463

Bravo AF: 0.859

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	10
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8045405; hg19: chr16-8503222;