rs887270

Variant names:

• chr19-2550854-G-A
• rs887270
• NM_052847.3:c.-38+4295C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.91).
• 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 rank	MANE	Protein	UniProt
GNG7	NM_052847.3	c.-38+4295C>T		intron_variant	Intron 3 of 4	ENST00000382159.8	NP_443079.1
GNG7	XM_047438629.1	c.-38+4295C>T		intron_variant	Intron 4 of 5		XP_047294585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNG7	ENST00000382159.8	c.-38+4295C>T		intron_variant	Intron 3 of 4	1	NM_052847.3	ENSP00000371594.2
GNG7	ENST00000587867.1	n.-38+4295C>T		intron_variant	Intron 3 of 5	5		ENSP00000468650.1

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

African (AFR) AF: 0.830 AC: 34435 AN: 41478

American (AMR) AF: 0.662 AC: 10108 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4322 AN: 5184

South Asian (SAS) AF: 0.688 AC: 3322 AN: 4826

European-Finnish (FIN) AF: 0.590 AC: 6240 AN: 10568

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36509 AN: 67938

Other (OTH) AF: 0.651 AC: 1368 AN: 2102

Alfa AF: 0.581 Hom.: 48171

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
PhyloP100		-2.7
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: rs887270; hg19: chr19-2550852;