rs2056531

Variant names:

• chr17-49205696-C-T
• rs2056531
• ENST00000503070.5:c.190+1081G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNGT2	ENST00000503070.5	c.190+1081G>A		intron_variant	Intron 3 of 3	3		ENSP00000420946.1

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

African (AFR) AF: 0.196 AC: 8116 AN: 41498

American (AMR) AF: 0.275 AC: 4207 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2290 AN: 5162

South Asian (SAS) AF: 0.201 AC: 967 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1111 AN: 10594

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12486 AN: 67994

Other (OTH) AF: 0.207 AC: 436 AN: 2104

Alfa AF: 0.197 Hom.: 3655

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
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2056531; hg19: chr17-47283058;