rs2519573

chr7-93770635-T-Achr7-93770635-T-G

Variant summary

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

The ENST00000455502.5(GNGT1):c.-55-115871T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,898 control chromosomes in the GnomAD database, including 46,545 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 0.78 (46545 hom., cov: 31)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

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=-0.68).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNGT1	ENST00000455502.5	c.-55-115871T>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118803 AN: 151780 Hom.: 46496 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.774

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: 0.764

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

GnomAD4 genome AF: 0.783 AC: 118910 AN: 151898 Hom.: 46545 Cov.: 31 AF XY: 0.786 AC XY: 58380 AN XY: 74240

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.764

Alfa AF: 0.730 Hom.: 2162

Bravo AF: 0.779

Asia WGS AF: 0.843 AC: 2916 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	2.7
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2519573; hg19: chr7-93399947;