chr17-50561532-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_018896.5(CACNA1G):c.73C>T(p.Leu25=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,538,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CACNA1G
NM_018896.5 synonymous
NM_018896.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.09
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 17-50561532-C-T is Benign according to our data. Variant chr17-50561532-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2962272.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.09 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000658 (10/152018) while in subpopulation EAS AF= 0.00195 (10/5118). AF 95% confidence interval is 0.00106. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1G | NM_018896.5 | c.73C>T | p.Leu25= | synonymous_variant | 1/38 | ENST00000359106.10 | |
CACNA1G-AS1 | NR_038439.1 | n.181+396G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1G | ENST00000359106.10 | c.73C>T | p.Leu25= | synonymous_variant | 1/38 | 1 | NM_018896.5 | A2 | |
CACNA1G-AS1 | ENST00000505793.1 | n.181+396G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 151900Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000668 AC: 9AN: 134778Hom.: 0 AF XY: 0.0000271 AC XY: 2AN XY: 73792
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GnomAD4 exome AF: 0.0000231 AC: 32AN: 1386050Hom.: 0 Cov.: 32 AF XY: 0.0000175 AC XY: 12AN XY: 684024
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GnomAD4 genome AF: 0.0000658 AC: 10AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74334
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 13, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at