rs2519580

Variant names:

• chr7-93766970-A-G
• rs2519580
• ENST00000926552.1:c.-55-119536A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455502.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000926552.1		c.-55-119536A>G		intron	N/A	ENSP00000596611.1
	GNGT1	ENST00000455502.5	TSL:2	c.-55-119536A>G		intron	N/A	ENSP00000395857.1	C9JGI9

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

African (AFR) AF: 0.787 AC: 32638 AN: 41472

American (AMR) AF: 0.815 AC: 12426 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2688 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4241 AN: 5122

South Asian (SAS) AF: 0.826 AC: 3987 AN: 4826

European-Finnish (FIN) AF: 0.823 AC: 8716 AN: 10592

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52726 AN: 67930

Other (OTH) AF: 0.769 AC: 1625 AN: 2114

Alfa AF: 0.787 Hom.: 8182

Bravo AF: 0.787

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		-0.018
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2519580;

hg19: chr7-93396282;