rs10133203

Positions:

• chr14-51888669-A-G
• chr14-51888669-A-T

Variant summary

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

The NM_053064.5(GNG2):​c.-30+11012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,064 control chromosomes in the GnomAD database, including 7,671 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 0.30 (7671 hom., cov: 31)
• Consequence: GNG2 NM_053064.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

GNG2 (HGNC:4404): (G protein subunit gamma 2) This gene encodes one of the gamma subunits of a guanine nucleotide-binding protein. Such proteins are involved in signaling mechanisms across membranes. Various subunits forms heterodimers which then interact with the different signal molecules. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNG2	NM_053064.5	c.-30+11012A>G		intron_variant		ENST00000556766.6	NP_444292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG2	ENST00000556766.6	c.-30+11012A>G		intron_variant		1	NM_053064.5	ENSP00000451231	P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45606 AN: 151946 Hom.: 7678 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.300 AC: 45601 AN: 152064 Hom.: 7671 Cov.: 31 AF XY: 0.300 AC XY: 22270 AN XY: 74326

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.287

Alfa AF: 0.357 Hom.: 20377

Bravo AF: 0.283

Asia WGS AF: 0.262 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.33

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: rs10133203; hg19: chr14-52355387;