rs1636255

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-2853170-C-A
• chr7-2853170-C-T

Variant summary

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

The ENST00000715275.1(GNA12):​n.60+17454G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,032 control chromosomes in the GnomAD database, including 4,974 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 0.24 (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) 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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+17454G>T		intron	N/A
	GNA12	ENST00000715276.1		n.164-7038G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35807 AN: 151914 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.236 AC: 35807 AN: 152032 Hom.: 4974 Cov.: 32 AF XY: 0.239 AC XY: 17756 AN XY: 74300

African (AFR) AF: 0.0929 AC: 3854 AN: 41504

American (AMR) AF: 0.277 AC: 4233 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5172

South Asian (SAS) AF: 0.152 AC: 731 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3708 AN: 10524

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19770 AN: 67954

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.248 Hom.: 3126

Bravo AF: 0.224

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.38
PhyloP100		-0.22

Splicing

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.

Other links and lift over

dbSNP: rs1636255;

hg19: chr7-2892804;