16-56960616-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 0.289 in 480,014 control chromosomes in the GnomAD database, including 21,163 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 (5583 hom., cov: 32)
  • Exomes 𝑓: 0.30 (15580 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.258 AC: 39182 AN: 151978 Hom.: 5583 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.248

GnomAD3 exomes AF: 0.285 AC: 48146 AN: 168940 Hom.: 7161 AF XY: 0.292 AC XY: 26952 AN XY: 92434

Gnomad AFR exome AF: 0.132

Gnomad AMR exome AF: 0.309

Gnomad ASJ exome AF: 0.261

Gnomad EAS exome AF: 0.159

Gnomad SAS exome AF: 0.324

Gnomad FIN exome AF: 0.265

Gnomad NFE exome AF: 0.310

Gnomad OTH exome AF: 0.289

GnomAD4 exome AF: 0.303 AC: 99410 AN: 327918 Hom.: 15580 Cov.: 0 AF XY: 0.307 AC XY: 57511 AN XY: 187072

Gnomad4 AFR exome AF: 0.138

Gnomad4 AMR exome AF: 0.311

Gnomad4 ASJ exome AF: 0.260

Gnomad4 EAS exome AF: 0.162

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.316

Gnomad4 OTH exome AF: 0.285

GnomAD4 genome AF: 0.258 AC: 39182 AN: 152096 Hom.: 5583 Cov.: 32 AF XY: 0.257 AC XY: 19116 AN XY: 74352

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.244

Alfa AF: 0.227 Hom.: 990

Bravo AF: 0.251

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17231506; hg19: chr16-56994528; COSMIC: COSV52364891;