19-2550854-G-A

Position:

• chr19-2550854-G-A

Variant summary

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

The NM_052847.3(GNG7):​c.-38+4295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,026 control chromosomes in the GnomAD database, including 33,512 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 0.65 (33512 hom., cov: 32)
• Consequence: GNG7 NM_052847.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNG7	NM_052847.3	c.-38+4295C>T		intron_variant		ENST00000382159.8	NP_443079.1
GNG7	XM_047438629.1	c.-38+4295C>T		intron_variant			XP_047294585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG7	ENST00000382159.8	c.-38+4295C>T		intron_variant		1	NM_052847.3	ENSP00000371594	P1
GNG7	ENST00000587867.1	c.-38+4295C>T		intron_variant, NMD_transcript_variant		5		ENSP00000468650

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98881 AN: 151908 Hom.: 33463 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.651 AC: 98992 AN: 152026 Hom.: 33512 Cov.: 32 AF XY: 0.657 AC XY: 48830 AN XY: 74308

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.651

Alfa AF: 0.568 Hom.: 32638

Bravo AF: 0.665

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.40

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: rs887270; hg19: chr19-2550852;