rs2293215

Positions:

• chr17-49207321-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
GNGT2	NM_001198754.2	c.84+18G>A		intron_variant		ENST00000507680.6
GNGT2	NM_001198755.1	c.84+18G>A		intron_variant
GNGT2	NM_001198756.1	c.84+18G>A		intron_variant
GNGT2	NM_031498.2	c.84+18G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNGT2	ENST00000507680.6	c.84+18G>A		intron_variant		4	NM_001198754.2	P1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30681 AN: 152002 Hom.: 3457 Cov.: 31

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

GnomAD3 exomes AF: 0.223 AC: 56131 AN: 251182 Hom.: 7331 AF XY: 0.219 AC XY: 29686 AN XY: 135792

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 SAS exome AF: 0.196

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.: 27 AF XY: 0.200 AC XY: 141928 AN XY: 708122

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.187

Gnomad4 OTH exome AF: 0.204

GnomAD4 genome AF: 0.202 AC: 30717 AN: 152120 Hom.: 3470 Cov.: 31 AF XY: 0.204 AC XY: 15189 AN XY: 74372

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.210

Alfa AF: 0.195 Hom.: 4185

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
DANN	Benign	0.59

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: rs2293215; hg19: chr17-47284683; COSMIC: COSV55929827; COSMIC: COSV55929827;