Variant chr16-56960616-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.671

Variant links:

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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	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39182

AN:

151978

Hom.:

5583

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.307

AC XY:

57511

AN XY:

187072

show subpopulations

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.:

AF XY:

0.257

AC XY:

19116

AN XY:

74352

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over