Genetic Variant GNG7:c.-78+35400G>A (chr19-2610824-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052847.3(GNG7):c.-78+35400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,550 control chromosomes in the GnomAD database, including 6,300 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 0.28 ( 6299 hom., cov: 27)

Exomes 𝑓: 0.18 ( 1 hom. )

Consequence

GNG7
NM_052847.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.19

Publications

6 publications found

Variant links:

Genes affected

GNG7 (HGNC:4410): (G protein subunit gamma 7) Predicted to enable G-protein beta-subunit binding activity. Predicted to be involved in G protein-coupled receptor signaling pathway and regulation of adenylate cyclase activity. Predicted to act upstream of or within behavioral fear response; locomotory behavior; and receptor guanylyl cyclase signaling pathway. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

GNG7 links:

ENSG00000267412 (HGNC:):

ENSG00000267412 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052847.3. 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
	GNG7	NM_052847.3	MANE Select	c.-78+35400G>A		intron	N/A	NP_443079.1	O60262

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GNG7	ENST00000382159.8	TSL:1 MANE Select	c.-78+35400G>A	intron	N/A	ENSP00000371594.2	O60262
GNG7	ENST00000865485.1		c.-78+35400G>A	intron	N/A	ENSP00000535544.1
GNG7	ENST00000865486.1		c.-78+35400G>A	intron	N/A	ENSP00000535545.1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42350

AN:

151410

Hom.:

6293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.0328

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.254

GnomAD4 exome

AF:

0.182

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.280

AC:

42370

AN:

151528

Hom.:

6299

Cov.:

AF XY:

0.275

AC XY:

20361

AN XY:

74034

show subpopulations

African (AFR)

AF:

0.371

AC:

15289

AN:

41198

American (AMR)

AF:

0.179

AC:

2718

AN:

15216

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

845

AN:

3466

East Asian (EAS)

AF:

0.0329

AC:

170

AN:

5164

South Asian (SAS)

AF:

0.176

AC:

844

AN:

4788

European-Finnish (FIN)

AF:

0.265

AC:

2785

AN:

10508

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.278

AC:

18866

AN:

67894

Other (OTH)

AF:

0.251

AC:

526

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1501

3002

4503

6004

7505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.259

Hom.:

5569

Bravo

AF:

0.276

Asia WGS

AF:

0.113

AC:

395

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.1

(source)

DANN

Benign

0.53

PhyloP100

-3.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over