Variant rs10802805 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000391854.7(GNG4):c.*2783C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,152 control chromosomes in the GnomAD database, including 23,891 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 0.55 ( 23850 hom., cov: 31)

Exomes 𝑓: 0.52 ( 41 hom. )

Consequence

GNG4
ENST00000391854.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Variant links:

Genes affected

GNG4 (HGNC:4407): (G protein subunit gamma 4) Predicted to enable G-protein beta-subunit binding activity. Involved in negative regulation of cell growth. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

GNG4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNG4	NM_001098722.2 linkuse as main transcript	c.*2783C>T		3_prime_UTR_variant	4/4	ENST00000391854.7	NP_001092192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG4	ENST00000391854.7 linkuse as main transcript	c.*2783C>T		3_prime_UTR_variant	4/4	1	NM_001098722.2	ENSP00000375727	P1
GNG4	ENST00000450593.5 linkuse as main transcript	c.*2783C>T		3_prime_UTR_variant	4/4	4		ENSP00000398629	P1

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83687

AN:

151746

Hom.:

23837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.828

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.584

GnomAD4 exome

AF:

0.517

AC:

149

AN:

288

Hom.:

Cov.:

AF XY:

0.510

AC XY:

107

AN XY:

210

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.750

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.417

Gnomad4 NFE exome

AF:

0.510

Gnomad4 OTH exome

AF:

0.633

GnomAD4 genome

AF:

0.551

AC:

83731

AN:

151864

Hom.:

23850

Cov.:

AF XY:

0.554

AC XY:

41083

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.446

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.601

Gnomad4 EAS

AF:

0.828

Gnomad4 SAS

AF:

0.449

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.590

Alfa

AF:

0.571

Hom.:

10918

Bravo

AF:

0.551

Asia WGS

AF:

0.622

AC:

2164

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.067

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over