rs35150881

Positions:

• chr19-2621195-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG7	NM_052847.3	c.-78+25029T>C		intron_variant		ENST00000382159.8
GNG7	XM_047438629.1	c.-78+25029T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG7	ENST00000382159.8	c.-78+25029T>C		intron_variant		1	NM_052847.3	P1
GNG7	ENST00000587867.1	c.-78+25029T>C		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0634

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0990 Hom.: 282

Bravo AF: 0.155

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs35150881; hg19: chr19-2621193;