NM_001378615.1:c.3288+25T>C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001378615.1(CC2D2A):c.3288+25T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000969 in 1,589,592 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001378615.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CC2D2A | NM_001378615.1 | c.3288+25T>C | intron_variant | Intron 25 of 36 | ENST00000424120.6 | NP_001365544.1 | ||
CC2D2A | NM_001080522.2 | c.3288+25T>C | intron_variant | Intron 26 of 37 | NP_001073991.2 | |||
CC2D2A | NM_001378617.1 | c.3141+25T>C | intron_variant | Intron 23 of 34 | NP_001365546.1 | |||
LOC124900671 | XR_007058061.1 | n.130+3224A>G | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00257 AC: 391AN: 152176Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00145 AC: 347AN: 239466Hom.: 4 AF XY: 0.00137 AC XY: 178AN XY: 129972
GnomAD4 exome AF: 0.000799 AC: 1149AN: 1437298Hom.: 5 Cov.: 26 AF XY: 0.000831 AC XY: 595AN XY: 716166
GnomAD4 genome AF: 0.00257 AC: 392AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.00250 AC XY: 186AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:2
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at