rs180282

Variant names:

• chr7-93901734-C-G
• rs180282
• ENST00000455502.5:c.-11-5002C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-93901734-C-G
• chr7-93901734-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNGT1	ENST00000455502.5	c.-11-5002C>G		intron_variant	Intron 2 of 3	2		ENSP00000395857.1

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;