rs2519573

Variant names:

• chr7-93770635-T-A
• rs2519573
• ENST00000455502.5:c.-55-115871T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-93770635-T-A
• chr7-93770635-T-G

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-55-115871T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,898 control chromosomes in the GnomAD database, including 46,545 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 0.78 (46545 hom., cov: 31)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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.-55-115871T>A		intron_variant	Intron 1 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118803 AN: 151780 Hom.: 46496 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.783 AC: 118910 AN: 151898 Hom.: 46545 Cov.: 31 AF XY: 0.786 AC XY: 58380 AN XY: 74240

African (AFR) AF: 0.763 AC: 31617 AN: 41450

American (AMR) AF: 0.812 AC: 12379 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2686 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4257 AN: 5142

South Asian (SAS) AF: 0.826 AC: 3986 AN: 4824

European-Finnish (FIN) AF: 0.823 AC: 8686 AN: 10556

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52701 AN: 67890

Other (OTH) AF: 0.764 AC: 1608 AN: 2106

Alfa AF: 0.730 Hom.: 2162

Bravo AF: 0.779

Asia WGS AF: 0.843 AC: 2916 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.7
DANN	Benign	0.93
PhyloP100		0.25
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: rs2519573; hg19: chr7-93399947;