7-93750044-T-C

Variant names:

• chr7-93750044-T-C
• rs2724079
• ENST00000926552.1:c.-55-136462T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000926552.1		c.-55-136462T>C		intron	N/A	ENSP00000596611.1
	GNGT1	ENST00000455502.5	TSL:2	c.-55-136462T>C		intron	N/A	ENSP00000395857.1	C9JGI9

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

African (AFR) AF: 0.790 AC: 32710 AN: 41392

American (AMR) AF: 0.812 AC: 12330 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2682 AN: 3466

East Asian (EAS) AF: 0.828 AC: 4246 AN: 5126

South Asian (SAS) AF: 0.827 AC: 3988 AN: 4820

European-Finnish (FIN) AF: 0.822 AC: 8698 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52595 AN: 67756

Other (OTH) AF: 0.769 AC: 1616 AN: 2102

Alfa AF: 0.788 Hom.: 8205

Bravo AF: 0.788

Asia WGS AF: 0.845 AC: 2938 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.71
PhyloP100		-2.1
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: rs2724079; hg19: chr7-93379356;