16-58663882-C-T

Variant names:

• chr16-58663882-C-T
• rs8061077

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 0.205 in 152,002 control chromosomes in the GnomAD database, including 3,198 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 0.20 (3198 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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: 0.204 AC: 31047 AN: 151884 Hom.: 3186 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.205 AC: 31095 AN: 152002 Hom.: 3198 Cov.: 33 AF XY: 0.203 AC XY: 15063 AN XY: 74282

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.190

Alfa AF: 0.201 Hom.: 6470

Bravo AF: 0.202

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8061077; hg19: chr16-58697786;