rs2056531

Positions:

• chr17-49205696-C-T

Variant summary

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

The ENST00000503070.5(GNGT2):​c.190+1081G>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 152,126 control chromosomes in the GnomAD database, including 3,460 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 (3460 hom., cov: 31)
• Consequence: GNGT2 ENST00000503070.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNGT2	ENST00000503070.5	c.190+1081G>A		intron_variant		3		ENSP00000420946

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30591 AN: 152008 Hom.: 3448 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.201 AC: 30625 AN: 152126 Hom.: 3460 Cov.: 31 AF XY: 0.204 AC XY: 15154 AN XY: 74358

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.207

Alfa AF: 0.195 Hom.: 2797

Bravo AF: 0.216

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2056531; hg19: chr17-47283058;