rs1316298

chr14-51899056-A-Gchr14-51899056-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+21399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,060 control chromosomes in the GnomAD database, including 9,746 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 0.35 (9746 hom., cov: 32)
• Consequence: GNG2 NM_053064.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG2	NM_053064.5	c.-30+21399A>G		intron_variant		ENST00000556766.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG2	ENST00000556766.6	c.-30+21399A>G		intron_variant		1	NM_053064.5	P1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53671 AN: 151942 Hom.: 9749 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53687 AN: 152060 Hom.: 9746 Cov.: 32 AF XY: 0.351 AC XY: 26127 AN XY: 74330

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.348

Alfa AF: 0.371 Hom.: 10304

Bravo AF: 0.350

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	2.2
Dann	Benign	0.89

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: rs1316298; hg19: chr14-52365774;