chr7-93701245-T-C

Position:

• chr7-93701245-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNGT1	ENST00000455502.5	c.-56+109474T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.626

Alfa AF: 0.600 Hom.: 6147

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10243929; hg19: chr7-93330557;