chr19-2547017-A-C

Position:

• chr19-2547017-A-C

Variant summary

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

The NM_052847.3(GNG7):​c.-38+8132T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,622 control chromosomes in the GnomAD database, including 1,299 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 0.12 (1299 hom., cov: 31)
• Consequence: GNG7 NM_052847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNG7	NM_052847.3	c.-38+8132T>G		intron_variant		ENST00000382159.8
GNG7	XM_047438629.1	c.-38+8132T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNG7	ENST00000382159.8	c.-38+8132T>G		intron_variant		1	NM_052847.3	P1
GNG7	ENST00000587867.1	c.-38+8132T>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18845 AN: 151504 Hom.: 1297 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.124 AC: 18872 AN: 151622 Hom.: 1299 Cov.: 31 AF XY: 0.125 AC XY: 9255 AN XY: 74106

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0965 Hom.: 1580

Bravo AF: 0.125

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.28

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: rs6510683; hg19: chr19-2547015;