Variant 16-56191113-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000662188.1(GNAO1-DT):n.6C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 149,266 control chromosomes in the GnomAD database, including 37,415 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 37407 hom., cov: 30)

Exomes 𝑓: 0.81 ( 8 hom. )

Consequence

GNAO1-DT
ENST00000662188.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.76

Variant links:

Genes affected

GNAO1-DT (HGNC:27543): (GNAO1 divergent transcript)

GNAO1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 16-56191113-G-A is Benign according to our data. Variant chr16-56191113-G-A is described in ClinVar as [Benign]. Clinvar id is 1283647.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAO1-DT	NR_027078.2 link	n.-19C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAO1-DT	ENST00000662188.1 link	n.6C>T		non_coding_transcript_exon_variant	Exon 1 of 4
GNAO1-DT	ENST00000501259.5 link	n.-19C>T		upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.694

AC:

103536

AN:

149136

Hom.:

37407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.795

Gnomad AMR

AF:

0.710

Gnomad ASJ

AF:

0.781

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.774

Gnomad NFE

AF:

0.809

Gnomad OTH

AF:

0.731

GnomAD4 exome

AF:

0.808

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.833

GnomAD4 genome

AF:

0.694

AC:

103553

AN:

149240

Hom.:

37407

Cov.:

AF XY:

0.691

AC XY:

50344

AN XY:

72842

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.709

Gnomad4 ASJ

AF:

0.781

Gnomad4 EAS

AF:

0.580

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.778

Gnomad4 NFE

AF:

0.809

Gnomad4 OTH

AF:

0.727

Alfa

AF:

0.745

Hom.:

5285

Bravo

AF:

0.686

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 21, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.94

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over