chr7-93750044-T-C

Position:

• chr7-93750044-T-C

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-55-136462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 151,620 control chromosomes in the GnomAD database, including 47,366 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 0.79 (47366 hom., cov: 31)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNGT1	ENST00000455502.5	c.-55-136462T>C		intron_variant		2		ENSP00000395857

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119744 AN: 151502 Hom.: 47316 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.790 AC: 119854 AN: 151620 Hom.: 47366 Cov.: 31 AF XY: 0.793 AC XY: 58769 AN XY: 74084

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.769

Alfa AF: 0.788 Hom.: 7966

Bravo AF: 0.788

Asia WGS AF: 0.845 AC: 2938 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2724079; hg19: chr7-93379356;