chr19-54012115-T-A

Position:

• chr19-54012115-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_145814.2(CACNG6):​c.709T>A​(p.Cys237Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 30)
• Consequence: CACNG6 NM_145814.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.47

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 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35046417).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG6	NM_145814.2	c.709T>A	p.Cys237Ser	missense_variant	4/4	ENST00000252729.7
CACNG6	NM_145815.2	c.571T>A	p.Cys191Ser	missense_variant	3/3
CACNG6	NM_031897.3	c.496T>A	p.Cys166Ser	missense_variant	2/2
CACNG6	NR_102308.2	n.289T>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG6	ENST00000252729.7	c.709T>A	p.Cys237Ser	missense_variant	4/4	1	NM_145814.2	P1
CACNG6	ENST00000346968.2	c.571T>A	p.Cys191Ser	missense_variant	3/3	5
CACNG6	ENST00000352529.1	c.496T>A	p.Cys166Ser	missense_variant	2/2	5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 30

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2023

The c.709T>A (p.C237S) alteration is located in exon 4 (coding exon 4) of the CACNG6 gene. This alteration results from a T to A substitution at nucleotide position 709, causing the cysteine (C) at amino acid position 237 to be replaced by a serine (S). 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	0.20
BayesDel_addAF	Uncertain	0.044	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.10	.;T;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.60	T;T;T
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.35	T;T;T
MetaSVM	Benign	-0.84	T
MutationAssessor	Benign	1.3	.;L;.
MutationTaster	Benign	0.56	N;N;N
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-2.8	D;D;D
REVEL	Benign	0.16
Sift	Pathogenic	0.0	D;T;D
Sift4G	Benign	0.080	T;T;T
Polyphen		0.99	D;D;D
Vest4		0.27
MutPred		0.43		.;Gain of sheet (P = 0.0827);.;
MVP		0.79
MPC		1.4
ClinPred		0.95	D
GERP RS		3.8
Varity_R		0.17
gMVP		0.34

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-54515369;