rs11766496
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031468.4(CALN1):c.501+99792C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,858 control chromosomes in the GnomAD database, including 2,886 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 0.18 ( 2886 hom., cov: 30)
Consequence
CALN1
NM_031468.4 intron
NM_031468.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0700
Genes affected
CALN1 (HGNC:13248): (calneuron 1) This gene encodes a protein with high similarity to the calcium-binding proteins of the calmodulin family. The encoded protein contains two EF-hand domains and potential calcium-binding sites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
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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 = 0.278 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALN1 | NM_031468.4 | c.501+99792C>G | intron_variant | ENST00000395275.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALN1 | ENST00000395275.7 | c.501+99792C>G | intron_variant | 5 | NM_031468.4 | ||||
CALN1 | ENST00000329008.9 | c.375+99792C>G | intron_variant | 1 | P1 | ||||
CALN1 | ENST00000395276.6 | c.375+99792C>G | intron_variant | 1 | P1 | ||||
CALN1 | ENST00000431984.5 | c.375+99792C>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.178 AC: 27074AN: 151740Hom.: 2871 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.179 AC: 27122AN: 151858Hom.: 2886 Cov.: 30 AF XY: 0.181 AC XY: 13394AN XY: 74204
GnomAD4 genome
?
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27122
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30
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13394
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74204
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500
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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