rs541952457
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_017721.5(CC2D1A):c.513+6_513+12del variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0027 in 1,611,536 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 5 hom. )
Consequence
CC2D1A
NM_017721.5 splice_donor_5th_base, intron
NM_017721.5 splice_donor_5th_base, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.44
Genes affected
CC2D1A (HGNC:30237): (coiled-coil and C2 domain containing 1A) This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
?
Variant 19-13913305-AAGTGGGC-A is Benign according to our data. Variant chr19-13913305-AAGTGGGC-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 128612.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CC2D1A | NM_017721.5 | c.513+6_513+12del | splice_donor_5th_base_variant, intron_variant | ENST00000318003.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D1A | ENST00000318003.11 | c.513+6_513+12del | splice_donor_5th_base_variant, intron_variant | 1 | NM_017721.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00186 AC: 283AN: 152218Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00160 AC: 394AN: 245750Hom.: 1 AF XY: 0.00165 AC XY: 220AN XY: 133492
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GnomAD4 exome AF: 0.00279 AC: 4066AN: 1459200Hom.: 5 AF XY: 0.00266 AC XY: 1933AN XY: 725694
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GnomAD4 genome ? AF: 0.00186 AC: 283AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.00175 AC XY: 130AN XY: 74494
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 17, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 20, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at