15-94298718-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001385001.1(MCTP2):c.453A>G(p.Pro151=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,604,588 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00023 ( 7 hom. )
Consequence
MCTP2
NM_001385001.1 synonymous
NM_001385001.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.63
Genes affected
MCTP2 (HGNC:25636): (multiple C2 and transmembrane domain containing 2) Enables calcium ion binding activity. Predicted to be involved in regulation of neurotransmitter secretion. Located in cytosol and nucleoplasm. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 15-94298718-A-G is Benign according to our data. Variant chr15-94298718-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 743017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.63 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCTP2 | NM_001385001.1 | c.453A>G | p.Pro151= | synonymous_variant | 2/23 | ENST00000357742.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCTP2 | ENST00000357742.10 | c.453A>G | p.Pro151= | synonymous_variant | 2/23 | 1 | NM_001385001.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152114Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000448 AC: 107AN: 238840Hom.: 0 AF XY: 0.000616 AC XY: 80AN XY: 129790
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GnomAD4 exome AF: 0.000232 AC: 337AN: 1452356Hom.: 7 Cov.: 32 AF XY: 0.000317 AC XY: 229AN XY: 722592
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
MCTP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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