Variant chr1-235549778-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001098722.2(GNG4):c.*2331G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,114 control chromosomes in the GnomAD database, including 24,484 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 0.56 ( 24483 hom., cov: 33)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

GNG4
NM_001098722.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG4	NM_001098722.2 linkuse as main transcript	c.*2331G>A		3_prime_UTR_variant	4/4	ENST00000391854.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG4	ENST00000391854.7 linkuse as main transcript	c.*2331G>A		3_prime_UTR_variant	4/4	1	NM_001098722.2	P1
GNG4	ENST00000450593.5 linkuse as main transcript	c.*2331G>A		3_prime_UTR_variant	4/4	4		P1

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85102

AN:

151990

Hom.:

24471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.472

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.586

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

1.00

GnomAD4 genome

AF:

0.560

AC:

85148

AN:

152110

Hom.:

24483

Cov.:

AF XY:

0.562

AC XY:

41811

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.471

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.600

Gnomad4 EAS

AF:

0.827

Gnomad4 SAS

AF:

0.487

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.592

Alfa

AF:

0.572

Hom.:

4329

Bravo

AF:

0.559

Asia WGS

AF:

0.636

AC:

2214

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

DANN

Benign

0.59

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