19-53992915-G-A

Variant names:

• chr19-53992915-G-A
• rs1434492187
• NM_145814.2:c.38G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145814.2(CACNG6):​c.38G>A​(p.Arg13Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000008 in 1,250,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 8.0e-7 (0 hom.)
• Consequence: CACNG6 NM_145814.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.32

Genes affected

CACNG6 (HGNC:13625): (calcium voltage-gated channel auxiliary subunit gamma 6) Voltage-dependent calcium channels are composed of five subunits. The protein encoded by this gene represents one of these subunits, gamma, and is one of two known gamma subunit proteins. This particular gamma subunit is an integral membrane protein that is thought to stabilize the calcium channel in an inactive (closed) state. This gene is part of a functionally diverse eight-member protein subfamily of the PMP-22/EMP/MP20 family and is located in a cluster with two family members that function as transmembrane AMPA receptor regulatory proteins (TARPs). Alternative splicing results in multiple transcript variants. Variants in this gene have been associated with aspirin-intolerant asthma. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14647737).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG6	NM_145814.2	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 4	ENST00000252729.7	NP_665813.1
CACNG6	NM_145815.2	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 3		NP_665814.1
CACNG6	NM_031897.3	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 2		NP_114103.2
CACNG6	NR_102308.2	n.49+1718G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG6	ENST00000252729.7	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 4	1	NM_145814.2	ENSP00000252729.2
CACNG6	ENST00000346968.2	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 3	5		ENSP00000319097.2
CACNG6	ENST00000352529.1	c.38G>A	p.Arg13Gln	missense_variant	Exon 1 of 2	5		ENSP00000319135.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.00e-7 AC: 1 AN: 1250338 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 610406

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.88e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 03, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.38G>A (p.R13Q) alteration is located in exon 1 (coding exon 1) of the CACNG6 gene. This alteration results from a G to A substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	23
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.040	.;T;.
Eigen	Benign	0.14
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.79	T;T;T
M_CAP	Benign	0.061	D
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.9	.;M;.
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-0.070	N;N;N
REVEL	Benign	0.091
Sift	Benign	0.26	T;T;T
Sift4G	Benign	0.42	T;T;T
Polyphen		0.61	P;D;D
Vest4		0.17
MutPred		0.14		Loss of MoRF binding (P = 0.0707);Loss of MoRF binding (P = 0.0707);Loss of MoRF binding (P = 0.0707);
MVP		0.38
MPC		1.4
ClinPred		0.75	D
GERP RS		3.1
Varity_R		0.067
gMVP		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: rs1434492187; hg19: chr19-54496169;