19-2621195-A-G

Variant names:

• chr19-2621195-A-G
• rs35150881
• NM_052847.3:c.-78+25029T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052847.3(GNG7):​c.-78+25029T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,100 control chromosomes in the GnomAD database, including 3,019 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 0.15 (3019 hom., cov: 31)
• Consequence: GNG7 NM_052847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNG7	NM_052847.3	MANE Select	c.-78+25029T>C		intron	N/A	NP_443079.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNG7	ENST00000382159.8	TSL:1 MANE Select	c.-78+25029T>C		intron	N/A	ENSP00000371594.2
	GNG7	ENST00000587867.1	TSL:5	n.-78+25029T>C		intron	N/A	ENSP00000468650.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22176 AN: 151982 Hom.: 3019 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.146 AC: 22192 AN: 152100 Hom.: 3019 Cov.: 31 AF XY: 0.141 AC XY: 10462 AN XY: 74352

African (AFR) AF: 0.361 AC: 14932 AN: 41408

American (AMR) AF: 0.0617 AC: 943 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3470

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5182

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4824

European-Finnish (FIN) AF: 0.0634 AC: 672 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4838 AN: 67998

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.107 Hom.: 2648

Bravo AF: 0.155

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs35150881; hg19: chr19-2621193;