chr19-2610824-C-T

Position:

• chr19-2610824-C-T

Variant summary

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

The ENST00000382159.8(GNG7):​c.-78+35400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,550 control chromosomes in the GnomAD database, including 6,300 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 0.28 (6299 hom., cov: 27)
  • Exomes 𝑓: 0.18 (1 hom.)
• Consequence: GNG7 ENST00000382159.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNG7	NM_052847.3	c.-78+35400G>A		intron_variant		ENST00000382159.8	NP_443079.1
GNG7	XM_047438629.1	c.-78+35400G>A		intron_variant			XP_047294585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNG7	ENST00000382159.8	c.-78+35400G>A		intron_variant		1	NM_052847.3	ENSP00000371594	P1
	ENST00000590491.1	n.1039G>A		non_coding_transcript_exon_variant	1/1
GNG7	ENST00000587867.1	c.-78+35400G>A		intron_variant, NMD_transcript_variant		5		ENSP00000468650

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42350 AN: 151410 Hom.: 6293 Cov.: 27

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.182 AC: 4 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.280 AC: 42370 AN: 151528 Hom.: 6299 Cov.: 27 AF XY: 0.275 AC XY: 20361 AN XY: 74034

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.251

Alfa AF: 0.256 Hom.: 3250

Bravo AF: 0.276

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.53

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: rs8104096; hg19: chr19-2610822;