rs7799704

Variant names:

• chr7-93600228-G-A
• rs7799704
• ENST00000455502.5:c.-56+8457G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-93600228-G-A
• chr7-93600228-G-C
• chr7-93600228-G-T

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-56+8457G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,092 control chromosomes in the GnomAD database, including 31,601 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 0.62 (31601 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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+8457G>A		intron_variant	Intron 1 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94925 AN: 151972 Hom.: 31551 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.625 AC: 95038 AN: 152092 Hom.: 31601 Cov.: 32 AF XY: 0.619 AC XY: 45991 AN XY: 74344

African (AFR) AF: 0.864 AC: 35874 AN: 41524

American (AMR) AF: 0.543 AC: 8303 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3775 AN: 5172

South Asian (SAS) AF: 0.642 AC: 3101 AN: 4828

European-Finnish (FIN) AF: 0.427 AC: 4501 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35581 AN: 67962

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.585 Hom.: 4763

Bravo AF: 0.642

Asia WGS AF: 0.683 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		0.092
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: rs7799704; hg19: chr7-93229540;