ENST00000501259.5:n.-30C>T

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

2

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)

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-DTNR_027078.2 linkn.-30C>T upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNAO1-DTENST00000501259.5 linkn.-30C>T upstream_gene_variant 1
GNAO1-DTENST00000662188.1 linkn.-6C>T upstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.0820
AC:
12219
AN:
149002
Hom.:
552
Cov.:
31
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:
2
AN:
28
Hom.:
0
Cov.:
0
AF XY:
0.0455
AC XY:
1
AN XY:
22
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.:
31
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.:
77
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
14
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.

Other links and lift over

dbSNP: rs113827322; hg19: chr16-56225036; API