16-55058229-A-G

Variant names:

• chr16-55058229-A-G
• rs8060118

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 0.331 in 149,148 control chromosomes in the GnomAD database, including 8,924 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 0.33 (8924 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

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 (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.330 AC: 49251 AN: 149040 Hom.: 8919 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.331 AC: 49294 AN: 149148 Hom.: 8924 Cov.: 33 AF XY: 0.331 AC XY: 24163 AN XY: 72914

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.335

Alfa AF: 0.264 Hom.: 5452

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8060118; hg19: chr16-55092141;