7-2853170-C-A

Variant names:

• chr7-2853170-C-A
• rs1636255
• ENST00000715275.1:n.60+17454G>T

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The ENST00000715275.1(GNA12):n.60+17454G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000715275.1 is not a MANE Select or MANE Plus Clinical transcript for GNA12; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.236 (AC=35,807) in the gnomAD database across 152,032 control chromosomes, including 4,974 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.322. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4974 hom., cov: 32)
• Consequence: GNA12 ENST00000715275.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 8 publications found

Genes affected

GNA12 (HGNC:4380): (G protein subunit alpha 12) Enables G protein activity; protein phosphatase 2A binding activity; and protein phosphatase activator activity. Involved in Rho-activating G protein-coupled receptor signaling pathway; regulation of TOR signaling; and regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in several cellular components, including cytosol; lateral plasma membrane; and neuronal cell body. [provided by Alliance of Genome Resources, Jun 2026]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

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

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.3219 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

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

RefSeq Transcripts

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+17454G>T	intron	Intron 1 of 1	Prot:
	GNA12 ENST00000715276.1		n.164-7038G>T	intron	Intron 1 of 1	Prot:

GNA12 ENST00000715275.1

HGVSc / HGVSpn.60+17454G>T

Exon rankIntron 1 of 1

intron

Prot:

GNA12 ENST00000715276.1

HGVSc / HGVSpn.164-7038G>T

Exon rankIntron 1 of 1

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.236	AC:35807	Hom:4973	AN:151914	Cov:32
GnomAD4 genome	AF: 0.236	AC:35807	Hom:4974	AN:152032	Cov:32
TOPMed (Bravo)	AF: 0.224	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.242	AC:26506	Hom:3679	AN:109469	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.268	AC:628	Hom:83	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.331	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.287	AC:86	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.244	AC:850	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.313	AC:2261	Hom:	AN:7230	Cov:
Qatari Genome	AF: 0.148	AC:26	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.334	AC:41025	Hom:6856	AN:122670	Cov:
Turkish Variome	AF: 0.195	AC:302	Hom:31	AN:1546	Cov:
UK10K	AF: 0.297	AC:2243	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.327	AC:2931	Hom:487	AN:8960	Cov:

Showing 14 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	7.8
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.38
GPN-Star LLR	N/A	2.1
GPN-Star score	N/A	-0.52
PhyloP100	Benign	-0.22

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs1636255;

hg19: chr7-2892804;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar