rs180273

chr7-93908983-A-Gchr7-93908983-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021955.5(GNGT1):c.97-1807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,150 control chromosomes in the GnomAD database, including 51,720 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 0.82 (51720 hom., cov: 33)
• Consequence: GNGT1 NM_021955.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNGT1	NM_021955.5	c.97-1807A>G		intron_variant		ENST00000248572.10
GNGT1	NM_001329426.2	c.97-1807A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNGT1	ENST00000248572.10	c.97-1807A>G		intron_variant		1	NM_021955.5	P1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125251 AN: 152032 Hom.: 51676 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.824 AC: 125348 AN: 152150 Hom.: 51720 Cov.: 33 AF XY: 0.825 AC XY: 61380 AN XY: 74402

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.837

Alfa AF: 0.800 Hom.: 79401

Bravo AF: 0.829

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.025
Dann	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs180273; hg19: chr7-93538295;