rs1032582

Variant names:

• chr14-51966385-A-G
• rs1032582
• NM_053064.5:c.88-174A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-51966385-A-G
• chr14-51966385-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.88-174A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,192 control chromosomes in the GnomAD database, including 61,558 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 0.89 (61558 hom., cov: 31)
• Consequence: GNG2 NM_053064.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNG2	NM_053064.5	c.88-174A>G		intron_variant	Intron 3 of 3	ENST00000556766.6	NP_444292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG2	ENST00000556766.6	c.88-174A>G		intron_variant	Intron 3 of 3	1	NM_053064.5	ENSP00000451231.1

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135811 AN: 152072 Hom.: 61515 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.893 AC: 135902 AN: 152192 Hom.: 61558 Cov.: 31 AF XY: 0.886 AC XY: 65876 AN XY: 74388

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.894

Alfa AF: 0.912 Hom.: 11185

Bravo AF: 0.874

Asia WGS AF: 0.667 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.66

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: rs1032582; hg19: chr14-52433103; COSMIC: COSV58915189; COSMIC: COSV58915189;