Variant 16-51064516-G-C 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 0.315 in 357,250 control chromosomes in the GnomAD database, including 20,822 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 0.36 ( 11277 hom., cov: 32)

Exomes 𝑓: 0.28 ( 9545 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.531

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.51064516G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54952

AN:

151872

Hom.:

11250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.493

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.711

Gnomad SAS

AF:

0.533

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.387

GnomAD3 exomes

AF:

0.320

AC:

46120

AN:

144238

Hom.:

8703

AF XY:

0.323

AC XY:

26309

AN XY:

81364

show subpopulations

Gnomad AFR exome

AF:

0.451

Gnomad AMR exome

AF:

0.390

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.654

Gnomad SAS exome

AF:

0.476

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.232

Gnomad OTH exome

AF:

0.291

GnomAD4 exome

AF:

0.280

AC:

57395

AN:

205260

Hom.:

9545

Cov.:

AF XY:

0.294

AC XY:

35019

AN XY:

119276

show subpopulations

Gnomad4 AFR exome

AF:

0.375

Gnomad4 AMR exome

AF:

0.379

Gnomad4 ASJ exome

AF:

0.305

Gnomad4 EAS exome

AF:

0.612

Gnomad4 SAS exome

AF:

0.444

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.203

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.362

AC:

55030

AN:

151990

Hom.:

11277

Cov.:

AF XY:

0.368

AC XY:

27372

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.711

Gnomad4 SAS

AF:

0.532

Gnomad4 FIN

AF:

0.270

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.394

Alfa

AF:

0.289

Hom.:

4550

Bravo

AF:

0.379

Asia WGS

AF:

0.622

AC:

2163

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.58

DANN

Benign

0.64

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