chr3-50254353-G-A

Position:

• chr3-50254353-G-A

Variant summary

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

The NM_002070.4(GNAI2):​c.464+1169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,990 control chromosomes in the GnomAD database, including 13,054 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 0.33 (13054 hom., cov: 32)
• Consequence: GNAI2 NM_002070.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

GNAI2 (HGNC:4385): (G protein subunit alpha i2) The protein encoded by this gene is an alpha subunit of guanine nucleotide binding proteins (G proteins). The encoded protein contains the guanine nucleotide binding site and is involved in the hormonal regulation of adenylate cyclase. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNAI2	NM_002070.4	c.464+1169G>A		intron_variant		ENST00000313601.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAI2	ENST00000313601.11	c.464+1169G>A		intron_variant		1	NM_002070.4	P1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50451 AN: 151872 Hom.: 13003 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.333 AC: 50567 AN: 151990 Hom.: 13054 Cov.: 32 AF XY: 0.335 AC XY: 24874 AN XY: 74316

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.308

Alfa AF: 0.165 Hom.: 6979

Bravo AF: 0.374

Asia WGS AF: 0.362 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.69
DANN	Benign	0.31

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: rs2282751; hg19: chr3-50291785;