16-56191113-G-A

Variant names:

• chr16-56191113-G-A
• rs188870525
• ENST00000662188.1:n.6C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.76

Genes affected

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

ACMG classification

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	n.-19C>T		upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.694 AC: 103536 AN: 149136 Hom.: 37407 Cov.: 30

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: 21 AN: 26 Hom.: 8 Cov.: 0 AF XY: 0.833 AC XY: 15 AN XY: 18

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.694 AC: 103553 AN: 149240 Hom.: 37407 Cov.: 30 AF XY: 0.691 AC XY: 50344 AN XY: 72842

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

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	11
DANN	Benign	0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs188870525; hg19: chr16-56225025;