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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNG7	NM_052847.3 link	c.-78+35400G>A		intron_variant	Intron 2 of 4	ENST00000382159.8	NP_443079.1	O60262
GNG7	XM_047438629.1 link	c.-78+35400G>A		intron_variant	Intron 3 of 5		XP_047294585.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GNG7	ENST00000382159.8 link	c.-78+35400G>A	intron_variant	Intron 2 of 4	1	NM_052847.3	ENSP00000371594.2	O60262
ENSG00000267412	ENST00000590491.1 link	n.1039G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
GNG7	ENST00000587867.1 link	n.-78+35400G>A	intron_variant	Intron 2 of 5	5		ENSP00000468650.1	K7ESC6

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over