18-11759433-C-T

Position:

• chr18-11759433-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182978.4(GNAL):​c.624+5488C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,284 control chromosomes in the GnomAD database, including 5,475 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 0.21 (5475 hom., cov: 33)
• Consequence: GNAL NM_182978.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

GNAL (HGNC:4388): (G protein subunit alpha L) This gene encodes a stimulatory G protein alpha subunit which mediates odorant signaling in the olfactory epithelium. This protein couples dopamine type 1 receptors and adenosine A2A receptors and is widely expressed in the central nervous system. Mutations in this gene have been associated with dystonia 25 and this gene is located in a susceptibility region for bipolar disorder and schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNAL	NM_001369387.1	c.393+5488C>T		intron_variant		ENST00000423027.8
GNAL	NM_182978.4	c.624+5488C>T		intron_variant		ENST00000334049.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAL	ENST00000334049.11	c.624+5488C>T		intron_variant		1	NM_182978.4
GNAL	ENST00000423027.8	c.393+5488C>T		intron_variant		1	NM_001369387.1	P1
	ENST00000666417.1	n.3235G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31595 AN: 152166 Hom.: 5451 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.208 AC: 31667 AN: 152284 Hom.: 5475 Cov.: 33 AF XY: 0.202 AC XY: 15047 AN XY: 74478

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0414

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.188

Alfa AF: 0.127 Hom.: 2422

Bravo AF: 0.225

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.19

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

Publications

LitVar

Other links and lift over

dbSNP: rs9947295; hg19: chr18-11759432;