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. The variant received -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
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 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.88-174A>G		intron	N/A	NP_444292.1
	GNG2	NM_001243773.2		c.88-174A>G		intron	N/A	NP_001230702.1
	GNG2	NM_001243774.2		c.88-174A>G		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.88-174A>G		intron	N/A	ENSP00000451231.1
	GNG2	ENST00000556752.2	TSL:1	c.88-174A>G		intron	N/A	ENSP00000451576.1
	GNG2	ENST00000553299.5	TSL:1	n.1061-174A>G		intron	N/A

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

African (AFR) AF: 0.826 AC: 34280 AN: 41500

American (AMR) AF: 0.786 AC: 12024 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3262 AN: 3472

East Asian (EAS) AF: 0.547 AC: 2826 AN: 5164

South Asian (SAS) AF: 0.784 AC: 3781 AN: 4824

European-Finnish (FIN) AF: 0.950 AC: 10064 AN: 10590

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66587 AN: 68034

Other (OTH) AF: 0.894 AC: 1888 AN: 2112

Alfa AF: 0.885 Hom.: 25667

Bravo AF: 0.874

Asia WGS AF: 0.667 AC: 2319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		-0.015
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: rs1032582; hg19: chr14-52433103; COSMIC: COSV58915189; COSMIC: COSV58915189;