Genetic Variant GNGT1:c.-56+93044T>G (chr7-93684815-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000455502.5(GNGT1):c.-56+93044T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,962 control chromosomes in the GnomAD database, including 8,970 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 0.31 ( 8970 hom., cov: 32)

Consequence

GNGT1
ENST00000455502.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.78

Publications

0 publications found

Variant links:

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]

GNGT1 links:

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new If you want to explore the variant's impact on the transcript ENST00000455502.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455502.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000926552.1		c.-56+93044T>G		intron	N/A	ENSP00000596611.1
	GNGT1	ENST00000455502.5	TSL:2	c.-56+93044T>G		intron	N/A	ENSP00000395857.1	C9JGI9

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47593

AN:

151842

Hom.:

8972

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.295

Gnomad NFE

AF:

0.432

Gnomad OTH

AF:

0.311

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

GnomAD4 genome

AF:

0.313

AC:

47585

AN:

151962

Hom.:

8970

Cov.:

AF XY:

0.309

AC XY:

22922

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.117

AC:

4869

AN:

41470

American (AMR)

AF:

0.256

AC:

3902

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1293

AN:

3462

East Asian (EAS)

AF:

0.216

AC:

1115

AN:

5164

South Asian (SAS)

AF:

0.369

AC:

1769

AN:

4800

European-Finnish (FIN)

AF:

0.385

AC:

4056

AN:

10544

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.432

AC:

29368

AN:

67950

Other (OTH)

AF:

0.310

AC:

654

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1543

3086

4629

6172

7715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.311

Hom.:

5323

Bravo

AF:

0.293

Asia WGS

AF:

0.255

AC:

887

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.3

(source)

DANN

Benign

0.68

PhyloP100

1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over