7-80135161-A-G

Position:

• chr7-80135161-A-G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_002069.6(GNAI1):​c.1A>G​(p.Met1?) variant causes a start lost change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000073 in 1,368,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: GNAI1 NM_002069.6 start_lost
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 8.41

Genes affected

GNAI1 (HGNC:4384): (G protein subunit alpha i1) Guanine nucleotide binding proteins are heterotrimeric signal-transducing molecules consisting of alpha, beta, and gamma subunits. The alpha subunit binds guanine nucleotide, can hydrolyze GTP, and can interact with other proteins. The protein encoded by this gene represents the alpha subunit of an inhibitory complex. The encoded protein is part of a complex that responds to beta-adrenergic signals by inhibiting adenylate cyclase. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAI1	NM_002069.6	c.1A>G	p.Met1?	start_lost	1/8	ENST00000649796.2	NP_002060.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAI1	ENST00000649796.2	c.1A>G	p.Met1?	start_lost	1/8		NM_002069.6	ENSP00000497260.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.30e-7 AC: 1 AN: 1368986 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 679560

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.38e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Developmental disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine

Feb 07, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.42
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.80	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.
Eigen	Uncertain	0.19
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.90	.;.;.;.;.;.;.;.;.;.;.;.;.;.;D;D
M_CAP	Pathogenic	0.98	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.00010	D
PROVEAN	Uncertain	-4.0	.;.;.;.;.;.;.;.;.;.;D;.;.;N;.;.
REVEL	Pathogenic	0.83
Sift	Pathogenic	0.0	.;.;.;.;.;.;.;.;.;.;.;.;.;D;.;.
Sift4G	Uncertain	0.0060	.;.;.;.;.;.;.;.;.;.;.;.;.;D;.;.
Polyphen		0.65	P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;.
Vest4		0.89
MutPred		0.75		Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);Loss of phosphorylation at S6 (P = 0.1699);
MVP		0.99
ClinPred		0.99	D
GERP RS		3.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.95
gMVP		0.83

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-79764477;