7-80106723-T-G

Position:

• chr7-80106723-T-G

Variant summary

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

The ENST00000648663.1(GNAI1):​c.-534+444T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,086 control chromosomes in the GnomAD database, including 52,024 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 0.82 (52024 hom., cov: 32)
• Consequence: GNAI1 ENST00000648663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80106723T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAI1	ENST00000648663.1	c.-534+444T>G		intron_variant				ENSP00000497379.1
GNAI1	ENST00000649225.1	c.-248-27497T>G		intron_variant				ENSP00000496829.1

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125299 AN: 151968 Hom.: 51992 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125376 AN: 152086 Hom.: 52024 Cov.: 32 AF XY: 0.828 AC XY: 61586 AN XY: 74342

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.834

Alfa AF: 0.851 Hom.: 71088

Bravo AF: 0.820

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10248649; hg19: chr7-79736039;