dbSNP rs10802805: GNG4:c.*2783C>T (chr1-235549326-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001098722.2(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
NM_001098722.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Publications

6 publications found

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:

Genome browser will be placed here

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=-0.9).

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 rank	MANE	Protein	UniProt
GNG4	NM_001098722.2 link	c.*2783C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000391854.7	NP_001092192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG4	ENST00000391854.7 link	c.*2783C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_001098722.2	ENSP00000375727.2
GNG4	ENST00000450593.5 link	c.*2783C>T		3_prime_UTR_variant	Exon 4 of 4	4		ENSP00000398629.1

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

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.417

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.510

AC:

107

AN:

210

Other (OTH)

AF:

0.633

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.551

AC:

83731

AN:

151864

Hom.:

23850

Cov.:

AF XY:

0.554

AC XY:

41083

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.446

AC:

18465

AN:

41376

American (AMR)

AF:

0.615

AC:

9385

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.601

AC:

2086

AN:

3468

East Asian (EAS)

AF:

0.828

AC:

4287

AN:

5176

South Asian (SAS)

AF:

0.449

AC:

2156

AN:

4798

European-Finnish (FIN)

AF:

0.614

AC:

6465

AN:

10536

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.574

AC:

38986

AN:

67938

Other (OTH)

AF:

0.590

AC:

1243

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1832

3664

5495

7327

9159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.570

Hom.:

12769

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

(source)

DANN

Benign

0.76

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over