ENST00000455502.5:c.-56+93044T>G

Variant names:

• chr7-93684815-T-G
• rs10487230
• ENST00000455502.5:c.-56+93044T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455502.5(GNGT1):​c.-56+93044T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,962 control chromosomes in the GnomAD database, including 8,970 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 0.31 (8970 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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+93044T>G		intron_variant	Intron 1 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47593 AN: 151842 Hom.: 8972 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47585 AN: 151962 Hom.: 8970 Cov.: 32 AF XY: 0.309 AC XY: 22922 AN XY: 74270

African (AFR) AF: 0.117 AC: 4869 AN: 41470

American (AMR) AF: 0.256 AC: 3902 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5164

South Asian (SAS) AF: 0.369 AC: 1769 AN: 4800

European-Finnish (FIN) AF: 0.385 AC: 4056 AN: 10544

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29368 AN: 67950

Other (OTH) AF: 0.310 AC: 654 AN: 2110

Alfa AF: 0.311 Hom.: 5323

Bravo AF: 0.293

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.68
PhyloP100		1.8
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: rs10487230; hg19: chr7-93314127;