rs1182179

Positions:

• chr7-2834014-A-G

Variant summary

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

The NM_007353.3(GNA12):​c.309+9839T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,144 control chromosomes in the GnomAD database, including 5,284 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 0.25 (5284 hom., cov: 32)
• Consequence: GNA12 NM_007353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

GNA12 (HGNC:4380): (G protein subunit alpha 12) Predicted to enable D5 dopamine receptor binding activity; G-protein beta/gamma-subunit complex binding activity; and GTPase activity. Involved in regulation of TOR signaling and regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNA12	NM_007353.3	c.309+9839T>C		intron_variant		ENST00000275364.8	NP_031379.2
GNA12	NM_001293092.2	c.309+9839T>C		intron_variant			NP_001280021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNA12	ENST00000275364.8	c.309+9839T>C		intron_variant		1	NM_007353.3	ENSP00000275364	P1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37899 AN: 152028 Hom.: 5282 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.249 AC: 37914 AN: 152144 Hom.: 5284 Cov.: 32 AF XY: 0.252 AC XY: 18711 AN XY: 74368

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.251

Alfa AF: 0.286 Hom.: 8494

Bravo AF: 0.238

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.040
DANN	Benign	0.52

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: rs1182179; hg19: chr7-2873648;