rs2048137

chr17-66871338-T-G

Variant summary

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

The NM_145811.3(CACNG5):c.-103-5892T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,864 control chromosomes in the GnomAD database, including 20,431 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 0.51 (20431 hom., cov: 31)
• Consequence: CACNG5 NM_145811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG5	NM_145811.3	c.-103-5892T>G		intron_variant		ENST00000533854.6
CACNG5	NM_001371476.1	c.-103-5892T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG5	ENST00000533854.6	c.-103-5892T>G		intron_variant		2	NM_145811.3	P1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77550 AN: 151746 Hom.: 20400 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.511 AC: 77642 AN: 151864 Hom.: 20431 Cov.: 31 AF XY: 0.508 AC XY: 37694 AN XY: 74228

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.494

Alfa AF: 0.523 Hom.: 4800

Bravo AF: 0.502

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.7
Dann	Benign	0.84

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: rs2048137; hg19: chr17-64867456;