16-58663882-C-T

Position:

• chr16-58663882-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;