rs3810244
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145814.2(CACNG6):c.-200A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 374,080 control chromosomes in the GnomAD database, including 84,908 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 0.68 ( 35273 hom., cov: 30)
Exomes 𝑓: 0.67 ( 49635 hom. )
Consequence
CACNG6
NM_145814.2 5_prime_UTR
NM_145814.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.284
Genes affected
CACNG6 (HGNC:13625): (calcium voltage-gated channel auxiliary subunit gamma 6) Voltage-dependent calcium channels are composed of five subunits. The protein encoded by this gene represents one of these subunits, gamma, and is one of two known gamma subunit proteins. This particular gamma subunit is an integral membrane protein that is thought to stabilize the calcium channel in an inactive (closed) state. 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 that function as transmembrane AMPA receptor regulatory proteins (TARPs). Alternative splicing results in multiple transcript variants. Variants in this gene have been associated with aspirin-intolerant asthma. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNG6 | NM_145814.2 | c.-200A>G | 5_prime_UTR_variant | 1/4 | ENST00000252729.7 | ||
CACNG6 | NM_031897.3 | c.-200A>G | 5_prime_UTR_variant | 1/2 | |||
CACNG6 | NM_145815.2 | c.-200A>G | 5_prime_UTR_variant | 1/3 | |||
CACNG6 | NR_102308.2 | n.49+1481A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNG6 | ENST00000252729.7 | c.-200A>G | 5_prime_UTR_variant | 1/4 | 1 | NM_145814.2 | P1 | ||
CACNG6 | ENST00000352529.1 | c.-200A>G | 5_prime_UTR_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.680 AC: 103234AN: 151736Hom.: 35241 Cov.: 30
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GnomAD4 exome AF: 0.667 AC: 148158AN: 222226Hom.: 49635 Cov.: 3 AF XY: 0.668 AC XY: 75457AN XY: 112994
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GnomAD4 genome ? AF: 0.680 AC: 103319AN: 151854Hom.: 35273 Cov.: 30 AF XY: 0.675 AC XY: 50085AN XY: 74212
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ClinVar
Not reported inComputational scores
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Name
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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