16-56313560-T-G

Variant names:

• chr16-56313560-T-G
• rs2587888
• NM_020988.3:c.304-15071T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020988.3(GNAO1):​c.304-15071T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,922 control chromosomes in the GnomAD database, including 14,810 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 0.43 (14810 hom., cov: 31)
• Consequence: GNAO1 NM_020988.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 8 publications found

Genes affected

GNAO1 (HGNC:4389): (G protein subunit alpha o1) The protein encoded by this gene represents the alpha subunit of the Go heterotrimeric G-protein signal-transducing complex. Defects in this gene are a cause of early-onset epileptic encephalopathy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

GNAO1 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 17

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
• movement disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, Illumina
• neurodevelopmental disorder with involuntary movements

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020988.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAO1	NM_020988.3	MANE Select	c.304-15071T>G		intron	N/A	NP_066268.1
	GNAO1	NM_138736.3		c.304-15071T>G		intron	N/A	NP_620073.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAO1	ENST00000262493.12	TSL:1 MANE Select	c.304-15071T>G		intron	N/A	ENSP00000262493.6
	GNAO1	ENST00000262494.13	TSL:1	c.304-15071T>G		intron	N/A	ENSP00000262494.7
	GNAO1	ENST00000638705.1	TSL:1	c.304-15071T>G		intron	N/A	ENSP00000491223.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65495 AN: 151804 Hom.: 14804 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.431 AC: 65515 AN: 151922 Hom.: 14810 Cov.: 31 AF XY: 0.428 AC XY: 31754 AN XY: 74240

African (AFR) AF: 0.306 AC: 12670 AN: 41426

American (AMR) AF: 0.491 AC: 7491 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5168

South Asian (SAS) AF: 0.493 AC: 2367 AN: 4800

European-Finnish (FIN) AF: 0.379 AC: 4003 AN: 10556

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33741 AN: 67934

Other (OTH) AF: 0.449 AC: 946 AN: 2106

Alfa AF: 0.485 Hom.: 30292

Bravo AF: 0.438

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2587888; hg19: chr16-56347472;