rs3810244

Variant names:

• chr19-53992678-A-G
• rs3810244
• NM_145814.2:c.-200A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-53992678-A-G
• chr19-53992678-A-T

Variant summary

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

The NM_145814.2(CACNG6):​c.-200A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 374,080 control chromosomes in the GnomAD database, including 84,908 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 0.68 (35273 hom., cov: 30)
  • Exomes 𝑓: 0.67 (49635 hom.)
• Consequence: CACNG6 NM_145814.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 18 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG6	NM_145814.2	c.-200A>G		5_prime_UTR_variant	Exon 1 of 4	ENST00000252729.7	NP_665813.1
CACNG6	NM_145815.2	c.-200A>G		5_prime_UTR_variant	Exon 1 of 3		NP_665814.1
CACNG6	NM_031897.3	c.-200A>G		5_prime_UTR_variant	Exon 1 of 2		NP_114103.2
CACNG6	NR_102308.2	n.49+1481A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG6	ENST00000252729.7	c.-200A>G		5_prime_UTR_variant	Exon 1 of 4	1	NM_145814.2	ENSP00000252729.2
CACNG6	ENST00000352529.1	c.-200A>G		5_prime_UTR_variant	Exon 1 of 2	5		ENSP00000319135.1
CACNG6	ENST00000346968.2	c.-200A>G		upstream_gene_variant		5		ENSP00000319097.2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103234 AN: 151736 Hom.: 35241 Cov.: 30

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.683

GnomAD4 exome AF: 0.667 AC: 148158 AN: 222226 Hom.: 49635 Cov.: 3 AF XY: 0.668 AC XY: 75457 AN XY: 112994

African (AFR) AF: 0.747 AC: 4548 AN: 6092

American (AMR) AF: 0.630 AC: 4025 AN: 6388

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 5859 AN: 7882

East Asian (EAS) AF: 0.694 AC: 14083 AN: 20290

South Asian (SAS) AF: 0.691 AC: 1582 AN: 2290

European-Finnish (FIN) AF: 0.571 AC: 11272 AN: 19748

Middle Eastern (MID) AF: 0.742 AC: 880 AN: 1186

European-Non Finnish (NFE) AF: 0.667 AC: 96054 AN: 143920

Other (OTH) AF: 0.683 AC: 9855 AN: 14430

GnomAD4 genome AF: 0.680 AC: 103319 AN: 151854 Hom.: 35273 Cov.: 30 AF XY: 0.675 AC XY: 50085 AN XY: 74212

African (AFR) AF: 0.741 AC: 30709 AN: 41426

American (AMR) AF: 0.639 AC: 9766 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2595 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3677 AN: 5120

South Asian (SAS) AF: 0.691 AC: 3333 AN: 4820

European-Finnish (FIN) AF: 0.564 AC: 5956 AN: 10560

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44951 AN: 67870

Other (OTH) AF: 0.686 AC: 1448 AN: 2110

Alfa AF: 0.672 Hom.: 117664

Bravo AF: 0.691

Asia WGS AF: 0.715 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.25
PhyloP100		-0.28
PromoterAI		0.015	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3810244; hg19: chr19-54495932;