17-50561825-TG-T

Position:

• chr17-50561825-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018896.5(CACNA1G):​c.242+134del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.057 (16 hom., cov: 18)
  • Exomes 𝑓: 0.18 (41 hom.)
  • Failed GnomAD Quality Control
• Consequence: CACNA1G NM_018896.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.207

Genes affected

CACNA1G (HGNC:1394): (calcium voltage-gated channel subunit alpha1 G) Voltage-sensitive calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division, and cell death. This gene encodes a T-type, low-voltage activated calcium channel. The T-type channels generate currents that are both transient, owing to fast inactivation, and tiny, owing to small conductance. T-type channels are thought to be involved in pacemaker activity, low-threshold calcium spikes, neuronal oscillations and resonance, and rebound burst firing. Many alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2011]

CACNA1G-AS1 (HGNC:27377): (CACNA1G antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-50561825-TG-T is Benign according to our data. Variant chr17-50561825-TG-T is described in ClinVar as [Benign]. Clinvar id is 1259361.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1G	NM_018896.5	c.242+134del		intron_variant		ENST00000359106.10
CACNA1G-AS1	NR_038439.1	n.181+102del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1G	ENST00000359106.10	c.242+134del		intron_variant		1	NM_018896.5	A2
CACNA1G-AS1	ENST00000505793.1	n.181+102del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 951 AN: 16694 Hom.: 16 Cov.: 18

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0380

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.184 AC: 157 AN: 852 Hom.: 41 Cov.: 8 AF XY: 0.186 AC XY: 80 AN XY: 430

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.550

Gnomad4 ASJ exome AF: 0.0833

Gnomad4 EAS exome AF: 0.572

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0160

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.0570 AC: 952 AN: 16712 Hom.: 16 Cov.: 18 AF XY: 0.0583 AC XY: 454 AN XY: 7790

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0117

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.0431

Gnomad4 OTH AF: 0.0380

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 28, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs370134471; hg19: chr17-48639186;