rs2519580

Positions:

• chr7-93766970-A-G

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-55-119536A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 151,982 control chromosomes in the GnomAD database, including 47,394 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 0.79 (47394 hom., cov: 31)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

GNGT1 (HGNC:4411): (G protein subunit gamma transducin 1) This gene encodes the gamma subunit of transducin, a guanine nucleotide-binding protein (G protein) that is found in rod outer segments. Transducin, also known as GMPase, mediates the activation of a cyclic GTP-specific (guanosine monophosphate) phosphodiesterase by rhodopsin. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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
GNGT1	ENST00000455502.5	c.-55-119536A>G		intron_variant		2		ENSP00000395857

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119927 AN: 151864 Hom.: 47343 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.790 AC: 120037 AN: 151982 Hom.: 47394 Cov.: 31 AF XY: 0.793 AC XY: 58867 AN XY: 74272

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.769

Alfa AF: 0.788 Hom.: 7946

Bravo AF: 0.787

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2519580; hg19: chr7-93396282;