dbSNP rs2293215: GNGT2:c.84+18G>A (chr17-49207321-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001198754.2(GNGT2):c.84+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,570,442 control chromosomes in the GnomAD database, including 35,607 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 0.20 ( 3470 hom., cov: 31)

Exomes 𝑓: 0.20 ( 32137 hom. )

Consequence

GNGT2
NM_001198754.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.687

Publications

13 publications found

Variant links:

Genes affected

GNGT2 (HGNC:4412): (G protein subunit gamma transducin 2) Phototransduction in rod and cone photoreceptors is regulated by groups of signaling proteins. The encoded protein is thought to play a crucial role in cone phototransduction. It belongs to the G protein gamma family and localized specifically in cones. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Nov 2010]

GNGT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GNGT2	NM_001198754.2 link	c.84+18G>A	intron_variant	Intron 3 of 3	ENST00000507680.6	NP_001185683.1	O14610
GNGT2	NM_001198755.1 link	c.84+18G>A	intron_variant	Intron 3 of 3		NP_001185684.1	O14610
GNGT2	NM_001198756.1 link	c.84+18G>A	intron_variant	Intron 3 of 3		NP_001185685.1	O14610
GNGT2	NM_031498.2 link	c.84+18G>A	intron_variant	Intron 3 of 3		NP_113686.1	O14610

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNGT2	ENST00000507680.6 link	c.84+18G>A		intron_variant	Intron 3 of 3	4	NM_001198754.2	ENSP00000421710.1		O14610

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30681

AN:

152002

Hom.:

3457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.206

GnomAD2 exomes

AF:

0.223

AC:

56131

AN:

251182

AF XY:

0.219

show subpopulations

Gnomad AFR exome

AF:

0.191

Gnomad AMR exome

AF:

0.334

Gnomad ASJ exome

AF:

0.235

Gnomad EAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.187

Gnomad OTH exome

AF:

0.207

GnomAD4 exome

AF:

0.201

AC:

284651

AN:

1418322

Hom.:

32137

Cov.:

AF XY:

0.200

AC XY:

141928

AN XY:

708122

show subpopulations

African (AFR)

AF:

0.192

AC:

6285

AN:

32654

American (AMR)

AF:

0.328

AC:

14651

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

6107

AN:

25898

East Asian (EAS)

AF:

0.512

AC:

20230

AN:

39488

South Asian (SAS)

AF:

0.198

AC:

16942

AN:

85438

European-Finnish (FIN)

AF:

0.119

AC:

6334

AN:

53398

Middle Eastern (MID)

AF:

0.237

AC:

1336

AN:

5634

European-Non Finnish (NFE)

AF:

0.187

AC:

200745

AN:

1072218

Other (OTH)

AF:

0.204

AC:

12021

AN:

58910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

10267

20533

30800

41066

51333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7206

14412

21618

28824

36030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.202

AC:

30717

AN:

152120

Hom.:

3470

Cov.:

AF XY:

0.204

AC XY:

15189

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.197

AC:

8183

AN:

41474

American (AMR)

AF:

0.275

AC:

4208

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.227

AC:

786

AN:

3466

East Asian (EAS)

AF:

0.442

AC:

2279

AN:

5154

South Asian (SAS)

AF:

0.200

AC:

964

AN:

4822

European-Finnish (FIN)

AF:

0.104

AC:

1106

AN:

10606

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12495

AN:

67994

Other (OTH)

AF:

0.210

AC:

444

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1227

2454

3681

4908

6135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.196

Hom.:

5301

Bravo

AF:

0.217

Asia WGS

AF:

0.297

AC:

1030

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.47

(source)

DANN

Benign

0.59

PhyloP100

-0.69

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over