rs180280

Variant names:

• chr7-93904151-G-A
• rs180280
• ENST00000455502.5:c.-11-2585G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-93904151-G-A
• chr7-93904151-G-C
• chr7-93904151-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.-11-2585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,244 control chromosomes in the GnomAD database, including 725 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 0.096 (725 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.129 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.-11-2585G>A		intron_variant	Intron 2 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14526 AN: 152126 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0956 AC: 14548 AN: 152244 Hom.: 725 Cov.: 32 AF XY: 0.0951 AC XY: 7082 AN XY: 74436

African (AFR) AF: 0.0881 AC: 3662 AN: 41560

American (AMR) AF: 0.134 AC: 2041 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.0804 AC: 416 AN: 5172

South Asian (SAS) AF: 0.107 AC: 517 AN: 4822

European-Finnish (FIN) AF: 0.0663 AC: 703 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6820 AN: 68004

Other (OTH) AF: 0.0836 AC: 177 AN: 2116

Alfa AF: 0.0982 Hom.: 1903

Bravo AF: 0.0951

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		0.57
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: rs180280; hg19: chr7-93533463;