14-51904595-T-C

Variant names:

• chr14-51904595-T-C
• rs11157866
• NM_053064.5:c.-30+26938T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053064.5. 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
	GNG2	NM_053064.5	MANE Select	c.-30+26938T>C		intron	N/A	NP_444292.1
	GNG2	NM_001243773.2		c.-30+26938T>C		intron	N/A	NP_001230702.1
	GNG2	NM_001243774.2		c.-30+43805T>C		intron	N/A	NP_001230703.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNG2	ENST00000556766.6	TSL:1 MANE Select	c.-30+26938T>C		intron	N/A	ENSP00000451231.1
	GNG2	ENST00000556752.2	TSL:1	c.-30+26938T>C		intron	N/A	ENSP00000451576.1
	GNG2	ENST00000553299.5	TSL:1	n.387+26938T>C		intron	N/A

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

African (AFR) AF: 0.823 AC: 34094 AN: 41448

American (AMR) AF: 0.858 AC: 13115 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2874 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5048 AN: 5178

South Asian (SAS) AF: 0.901 AC: 4341 AN: 4820

European-Finnish (FIN) AF: 0.938 AC: 9941 AN: 10594

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.883 AC: 60063 AN: 68008

Other (OTH) AF: 0.859 AC: 1812 AN: 2110

Alfa AF: 0.874 Hom.: 180293

Bravo AF: 0.860

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.79
PhyloP100		1.7
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: rs11157866; hg19: chr14-52371313;