Variant chr16-56961324-C-A 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 0.515 in 481,042 control chromosomes in the GnomAD database, including 64,531 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 0.52 ( 20884 hom., cov: 33)

Exomes 𝑓: 0.51 ( 43647 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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:

0.522

AC:

79285

AN:

151974

Hom.:

20854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.653

Gnomad AMR

AF:

0.506

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.499

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.502

GnomAD3 exomes

AF:

0.508

AC:

88585

AN:

174424

Hom.:

22587

AF XY:

0.511

AC XY:

48698

AN XY:

95346

show subpopulations

Gnomad AFR exome

AF:

0.558

Gnomad AMR exome

AF:

0.528

Gnomad ASJ exome

AF:

0.513

Gnomad EAS exome

AF:

0.491

Gnomad SAS exome

AF:

0.592

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.473

Gnomad OTH exome

AF:

0.500

GnomAD4 exome

AF:

0.512

AC:

168449

AN:

328950

Hom.:

43647

Cov.:

AF XY:

0.518

AC XY:

97232

AN XY:

187742

show subpopulations

Gnomad4 AFR exome

AF:

0.567

Gnomad4 AMR exome

AF:

0.528

Gnomad4 ASJ exome

AF:

0.511

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.490

Gnomad4 NFE exome

AF:

0.479

Gnomad4 OTH exome

AF:

0.504

GnomAD4 genome

AF:

0.522

AC:

79359

AN:

152092

Hom.:

20884

Cov.:

AF XY:

0.525

AC XY:

39066

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.506

Gnomad4 ASJ

AF:

0.504

Gnomad4 EAS

AF:

0.498

Gnomad4 SAS

AF:

0.601

Gnomad4 FIN

AF:

0.509

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.502

Alfa

AF:

0.497

Hom.:

41336

Bravo

AF:

0.522

Asia WGS

AF:

0.546

AC:

1902

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.41

DANN

Benign

0.66

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