rs180282

chr7-93901734-C-Gchr7-93901734-C-T

Variant summary

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

The ENST00000455502.5(GNGT1):c.-11-5002C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,046 control chromosomes in the GnomAD database, including 48,242 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 0.80 (48242 hom., cov: 31)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.827 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.-11-5002C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121005 AN: 151928 Hom.: 48214 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.796 AC: 121081 AN: 152046 Hom.: 48242 Cov.: 31 AF XY: 0.799 AC XY: 59348 AN XY: 74312

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.821

Alfa AF: 0.708 Hom.: 2293

Bravo AF: 0.798

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.93
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180282; hg19: chr7-93531046;