NM_001378615.1:c.4065+28A>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378615.1(CC2D2A):c.4065+28A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.992 in 1,395,038 control chromosomes in the GnomAD database, including 686,809 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001378615.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CC2D2A | NM_001378615.1 | c.4065+28A>T | intron_variant | Intron 31 of 36 | ENST00000424120.6 | NP_001365544.1 | ||
CC2D2A | NM_001080522.2 | c.4065+28A>T | intron_variant | Intron 32 of 37 | NP_001073991.2 | |||
CC2D2A | NM_001378617.1 | c.3918+28A>T | intron_variant | Intron 29 of 34 | NP_001365546.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.958 AC: 145776AN: 152178Hom.: 70128 Cov.: 31
GnomAD3 exomes AF: 0.990 AC: 205033AN: 207164Hom.: 101602 AF XY: 0.992 AC XY: 112364AN XY: 113240
GnomAD4 exome AF: 0.996 AC: 1237702AN: 1242742Hom.: 616635 Cov.: 16 AF XY: 0.996 AC XY: 616833AN XY: 619042
GnomAD4 genome AF: 0.958 AC: 145881AN: 152296Hom.: 70174 Cov.: 31 AF XY: 0.960 AC XY: 71458AN XY: 74460
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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Meckel syndrome, type 6 Benign:1
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Joubert syndrome 9 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at