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. The variant received -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
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.827 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000455502.5	TSL:2	c.-11-5002C>G		intron	N/A	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

African (AFR) AF: 0.783 AC: 32453 AN: 41460

American (AMR) AF: 0.839 AC: 12814 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2919 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4315 AN: 5160

South Asian (SAS) AF: 0.792 AC: 3812 AN: 4816

European-Finnish (FIN) AF: 0.817 AC: 8648 AN: 10580

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53388 AN: 67972

Other (OTH) AF: 0.821 AC: 1735 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.63
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs180282; hg19: chr7-93531046;