rs7780752

Variant names:

• chr7-93612328-T-C
• rs7780752
• ENST00000455502.5:c.-56+20557T>C

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-56+20557T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,826 control chromosomes in the GnomAD database, including 6,367 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 0.27 (6367 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 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.-56+20557T>C		intron_variant	Intron 1 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40763 AN: 151706 Hom.: 6367 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.269 AC: 40766 AN: 151826 Hom.: 6367 Cov.: 32 AF XY: 0.264 AC XY: 19581 AN XY: 74192

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.277

Alfa AF: 0.300 Hom.: 1317

Bravo AF: 0.256

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780752; hg19: chr7-93241640;