ENST00000455502.5:c.-56+109474T>C

Variant names:

• chr7-93701245-T-C
• rs10243929
• ENST00000455502.5:c.-56+109474T>C

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-56+109474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 133,878 control chromosomes in the GnomAD database, including 31,006 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 (31006 hom., cov: 21)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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+109474T>C		intron_variant	Intron 1 of 3	2		ENSP00000395857.1

Frequencies

GnomAD3 genomes AF: 0.620 AC: 82952 AN: 133790 Hom.: 30976 Cov.: 21

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.620 AC: 83025 AN: 133878 Hom.: 31006 Cov.: 21 AF XY: 0.620 AC XY: 40088 AN XY: 64682

African (AFR) AF: 0.743 AC: 26686 AN: 35910

American (AMR) AF: 0.526 AC: 6966 AN: 13240

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 1965 AN: 3138

East Asian (EAS) AF: 0.831 AC: 4212 AN: 5070

South Asian (SAS) AF: 0.666 AC: 2738 AN: 4110

European-Finnish (FIN) AF: 0.512 AC: 4263 AN: 8332

Middle Eastern (MID) AF: 0.595 AC: 150 AN: 252

European-Non Finnish (NFE) AF: 0.561 AC: 34328 AN: 61190

Other (OTH) AF: 0.626 AC: 1149 AN: 1834

Alfa AF: 0.600 Hom.: 6949

Asia WGS AF: 0.750 AC: 2575 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.30
PhyloP100		-0.43
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: rs10243929; hg19: chr7-93330557;