17-66864025-G-A

Variant names:

• chr17-66864025-G-A
• rs12602262
• NM_145811.3:c.-103-13205G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145811.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG5	NM_145811.3	MANE Select	c.-103-13205G>A		intron	N/A	NP_665810.1
	CACNG5	NM_001371476.1		c.-103-13205G>A		intron	N/A	NP_001358405.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG5	ENST00000533854.6	TSL:2 MANE Select	c.-103-13205G>A		intron	N/A	ENSP00000436836.1

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

African (AFR) AF: 0.0317 AC: 1316 AN: 41562

American (AMR) AF: 0.0444 AC: 678 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.135 AC: 697 AN: 5164

South Asian (SAS) AF: 0.0455 AC: 219 AN: 4816

European-Finnish (FIN) AF: 0.0409 AC: 433 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3857 AN: 68014

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0556 Hom.: 554

Bravo AF: 0.0500

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.40
PhyloP100		-1.1
Mutation Taster		=100/0	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: rs12602262; hg19: chr17-64860143;