Variant 16-51271296-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 0.0398 in 152,260 control chromosomes in the GnomAD database, including 259 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 0.040 ( 259 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.95

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.51271296C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285367	ENST00000642450.1 linkuse as main transcript	n.351-40274C>T	intron_variant
ENSG00000285367	ENST00000643626.1 linkuse as main transcript	n.52-40274C>T	intron_variant
ENSG00000285367	ENST00000644069.1 linkuse as main transcript	n.334-935C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0399

AC:

6070

AN:

152142

Hom.:

260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0478

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0757

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.0407

Gnomad FIN

AF:

0.0382

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.0368

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0398

AC:

6064

AN:

152260

Hom.:

259

Cov.:

AF XY:

0.0417

AC XY:

3105

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0478

Gnomad4 AMR

AF:

0.0755

Gnomad4 ASJ

AF:

0.0323

Gnomad4 EAS

AF:

0.237

Gnomad4 SAS

AF:

0.0401

Gnomad4 FIN

AF:

0.0382

Gnomad4 NFE

AF:

0.0132

Gnomad4 OTH

AF:

0.0383

Alfa

AF:

0.0227

Hom.:

Bravo

AF:

0.0452

Asia WGS

AF:

0.138

AC:

477

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.56

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