rs180280

chr7-93904151-G-Achr7-93904151-G-T

Variant summary

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

The ENST00000455502.5(GNGT1):c.-11-2585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,244 control chromosomes in the GnomAD database, including 725 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 0.096 (725 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.129 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.-11-2585G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14526 AN: 152126 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0956 AC: 14548 AN: 152244 Hom.: 725 Cov.: 32 AF XY: 0.0951 AC XY: 7082 AN XY: 74436

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0804

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0969 Hom.: 687

Bravo AF: 0.0951

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180280; hg19: chr7-93533463;