rs4334421

chr19-2580059-A-Gchr19-2580059-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052847.3(GNG7):c.-77-24871T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,840 control chromosomes in the GnomAD database, including 12,139 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 0.37 (12139 hom., cov: 31)
• Consequence: GNG7 NM_052847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG7	NM_052847.3	c.-77-24871T>C		intron_variant		ENST00000382159.8
GNG7	XM_047438629.1	c.-77-24871T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG7	ENST00000382159.8	c.-77-24871T>C		intron_variant		1	NM_052847.3	P1
GNG7	ENST00000587867.1	c.-77-24871T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56513 AN: 151722 Hom.: 12114 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.373 AC: 56578 AN: 151840 Hom.: 12139 Cov.: 31 AF XY: 0.376 AC XY: 27923 AN XY: 74210

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.340

Alfa AF: 0.256 Hom.: 9522

Bravo AF: 0.387

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.74

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: rs4334421; hg19: chr19-2580057;