Genetic Variant ENST00000501259.5:n.-30C>T (chr16-56191124-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The ENST00000501259.5(GNAO1-DT):n.-30C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 149,136 control chromosomes in the GnomAD database, including 553 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 553 hom., cov: 31)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

GNAO1-DT
ENST00000501259.5 upstream_gene

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0580

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=-0.76).

BP6

Variant 16-56191124-G-A is Benign according to our data. Variant chr16-56191124-G-A is described in ClinVar as [Benign]. Clinvar id is 1238856.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAO1-DT	NR_027078.2 link	n.-30C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAO1-DT	ENST00000501259.5 link	n.-30C>T		upstream_gene_variant		1
GNAO1-DT	ENST00000662188.1 link	n.-6C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0820

AC:

12219

AN:

149002

Hom.:

552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.0503

Gnomad ASJ

AF:

0.0461

Gnomad EAS

AF:

0.0342

Gnomad SAS

AF:

0.0937

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0321

Gnomad NFE

AF:

0.0754

Gnomad OTH

AF:

0.0586

GnomAD4 exome

AF:

0.0714

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0455

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0909

GnomAD4 genome

AF:

0.0820

AC:

12231

AN:

149108

Hom.:

553

Cov.:

AF XY:

0.0825

AC XY:

6006

AN XY:

72782

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.0506

Gnomad4 ASJ

AF:

0.0461

Gnomad4 EAS

AF:

0.0342

Gnomad4 SAS

AF:

0.0940

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.0754

Gnomad4 OTH

AF:

0.0580

Alfa

AF:

0.0792

Hom.:

Bravo

AF:

0.0755

Asia WGS

AF:

0.0730

AC:

247

AN:

3378

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 31, 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

-0.76

CADD

Benign

DANN

Benign

0.93

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