7-2865166-C-G

Variant names:

• chr7-2865166-C-G
• rs10487884
• ENST00000715275.1:n.60+5458G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715275.1(GNA12):​n.60+5458G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 151,942 control chromosomes in the GnomAD database, including 612 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 0.087 (612 hom., cov: 31)
• Consequence: GNA12 ENST00000715275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 4 publications found

Genes affected

GNA12 (HGNC:4380): (G protein subunit alpha 12) Predicted to enable D5 dopamine receptor binding activity; G-protein beta/gamma-subunit complex binding activity; and GTPase activity. Involved in regulation of TOR signaling and regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000293591 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNA12	ENST00000715275.1		n.60+5458G>C		intron	N/A
	GNA12	ENST00000715276.1		n.163+5458G>C		intron	N/A
	ENSG00000293591	ENST00000715277.1		n.*129C>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13242 AN: 151824 Hom.: 604 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0874 AC: 13275 AN: 151942 Hom.: 612 Cov.: 31 AF XY: 0.0846 AC XY: 6284 AN XY: 74246

African (AFR) AF: 0.106 AC: 4376 AN: 41408

American (AMR) AF: 0.0947 AC: 1444 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3468

East Asian (EAS) AF: 0.0990 AC: 510 AN: 5150

South Asian (SAS) AF: 0.0411 AC: 197 AN: 4796

European-Finnish (FIN) AF: 0.0485 AC: 513 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0828 AC: 5627 AN: 67982

Other (OTH) AF: 0.112 AC: 235 AN: 2104

Alfa AF: 0.0833 Hom.: 78

Bravo AF: 0.0958

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs10487884; hg19: chr7-2904800;