rs3972219

chr17-65022415-A-G

Variant summary

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

The NM_006572.6(GNA13):c.511-4112T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 151,676 control chromosomes in the GnomAD database, including 199 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 0.042 (199 hom., cov: 31)
• Consequence: GNA13 NM_006572.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

GNA13 (HGNC:4381): (G protein subunit alpha 13) Predicted to enable D5 dopamine receptor binding activity; G-protein beta/gamma-subunit complex binding activity; and GTPase activity. Predicted to be involved in several processes, including Rho protein signal transduction; activation of phospholipase D activity; and multicellular organism aging. Predicted to act upstream of or within several processes, including branching involved in blood vessel morphogenesis; negative regulation of vascular associated smooth muscle cell migration; and negative regulation of vascular associated smooth muscle cell proliferation. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNA13	NM_006572.6	c.511-4112T>C		intron_variant		ENST00000439174.7
GNA13	NM_001282425.2	c.226-4112T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA13	ENST00000439174.7	c.511-4112T>C		intron_variant		1	NM_006572.6	P1
GNA13	ENST00000541118.1	c.226-4112T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6424 AN: 151562 Hom.: 199 Cov.: 31

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0277

Gnomad ASJ AF: 0.0664

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0424 AC: 6427 AN: 151676 Hom.: 199 Cov.: 31 AF XY: 0.0422 AC XY: 3128 AN XY: 74120

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.0664

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0254

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0563 Hom.: 153

Bravo AF: 0.0386

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.20
Dann	Benign	0.37

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: rs3972219; hg19: chr17-63018533;