rs7780752

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 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.-56+20557T>C		intron	N/A	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

African (AFR) AF: 0.111 AC: 4586 AN: 41496

American (AMR) AF: 0.231 AC: 3520 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3460

East Asian (EAS) AF: 0.283 AC: 1448 AN: 5116

South Asian (SAS) AF: 0.377 AC: 1815 AN: 4808

European-Finnish (FIN) AF: 0.262 AC: 2765 AN: 10558

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24527 AN: 67854

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.321 Hom.: 15192

Bravo AF: 0.256

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.36
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: rs7780752; hg19: chr7-93241640;