Variant 16-85942053-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 0.735 in 152,184 control chromosomes in the GnomAD database, including 41,771 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 0.73 ( 41771 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.85942053C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000285163	ENST00000645383.1 linkuse as main transcript	n.394-3363C>T	intron_variant
ENSG00000285163	ENST00000646214.1 linkuse as main transcript	n.78-3363C>T	intron_variant
ENSG00000285163	ENST00000646986.1 linkuse as main transcript	n.716-3363C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.735

AC:

111712

AN:

152064

Hom.:

41712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.841

Gnomad AMI

AF:

0.608

Gnomad AMR

AF:

0.749

Gnomad ASJ

AF:

0.620

Gnomad EAS

AF:

0.863

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.658

Gnomad OTH

AF:

0.694

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

GnomAD4 genome

AF:

0.735

AC:

111838

AN:

152184

Hom.:

41771

Cov.:

AF XY:

0.741

AC XY:

55105

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.842

Gnomad4 AMR

AF:

0.749

Gnomad4 ASJ

AF:

0.620

Gnomad4 EAS

AF:

0.863

Gnomad4 SAS

AF:

0.763

Gnomad4 FIN

AF:

0.773

Gnomad4 NFE

AF:

0.658

Gnomad4 OTH

AF:

0.697

Alfa

AF:

0.668

Hom.:

76651

Bravo

AF:

0.738

Asia WGS

AF:

0.823

AC:

2860

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.38

DANN

Benign

0.67

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