7-80149921-T-C

Position:

• chr7-80149921-T-C

Variant summary

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

The NM_002069.6(GNAI1):​c.118+14643T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152,232 control chromosomes in the GnomAD database, including 219 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 0.043 (219 hom., cov: 32)
• Consequence: GNAI1 NM_002069.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

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]

GNAI1 (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 = 0.0977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAI1	NM_002069.6	c.118+14643T>C		intron_variant		ENST00000649796.2	NP_002060.4
GNAI1	NM_001256414.2	c.-39+13849T>C		intron_variant			NP_001243343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAI1	ENST00000649796.2	c.118+14643T>C		intron_variant			NM_002069.6	ENSP00000497260.1

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6476 AN: 152114 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.0639

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.00414

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0425 AC: 6476 AN: 152232 Hom.: 219 Cov.: 32 AF XY: 0.0415 AC XY: 3088 AN XY: 74444

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.0639

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.00414

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0138 Hom.: 13

Bravo AF: 0.0484

Asia WGS AF: 0.0450 AC: 158 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	1.5
DANN	Benign	0.44

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: rs10486928; hg19: chr7-79779237;