rs12602262

chr17-66864025-G-A

Variant summary

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

The NM_145811.3(CACNG5):c.-103-13205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 152,220 control chromosomes in the GnomAD database, including 223 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 0.050 (223 hom., cov: 33)
• Consequence: CACNG5 NM_145811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

CACNG5 (HGNC:1409): (calcium voltage-gated channel auxiliary subunit gamma 5) The protein encoded by this gene is a type II transmembrane AMPA receptor regulatory protein (TARP). TARPs regulate both trafficking and channel gating of the AMPA receptors. 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, a type I TARP and a calcium channel gamma subunit. This gene is a susceptibility locus for schizophrenia and bipolar disorder. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG5	NM_145811.3	c.-103-13205G>A		intron_variant		ENST00000533854.6
CACNG5	NM_001371476.1	c.-103-13205G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG5	ENST00000533854.6	c.-103-13205G>A		intron_variant		2	NM_145811.3	P1

Frequencies

GnomAD3 genomes AF: 0.0503 AC: 7645 AN: 152102 Hom.: 223 Cov.: 33

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0444

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0502 AC: 7641 AN: 152220 Hom.: 223 Cov.: 33 AF XY: 0.0495 AC XY: 3686 AN XY: 74420

Gnomad4 AFR AF: 0.0317

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.0802

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.0409

Gnomad4 NFE AF: 0.0567

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0538 Hom.: 101

Bravo AF: 0.0500

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.24
Dann	Benign	0.40

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: rs12602262; hg19: chr17-64860143;