rs11157866

chr14-51904595-T-C

Variant summary

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

The NM_053064.5(GNG2):c.-30+26938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,118 control chromosomes in the GnomAD database, including 57,685 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 0.87 (57685 hom., cov: 30)
• Consequence: GNG2 NM_053064.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG2	NM_053064.5	c.-30+26938T>C		intron_variant		ENST00000556766.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG2	ENST00000556766.6	c.-30+26938T>C		intron_variant		1	NM_053064.5	P1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132247 AN: 152000 Hom.: 57651 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.870 AC: 132332 AN: 152118 Hom.: 57685 Cov.: 30 AF XY: 0.873 AC XY: 64935 AN XY: 74352

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.859

Alfa AF: 0.872 Hom.: 75670

Bravo AF: 0.860

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.1
Dann	Benign	0.79

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: rs11157866; hg19: chr14-52371313;