rs886038409
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001378615.1(CC2D2A):c.3594+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000423 in 1,419,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001378615.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CC2D2A | NM_001378615.1 | c.3594+8T>C | splice_region_variant, intron_variant | ENST00000424120.6 | NP_001365544.1 | |||
LOC124900671 | XR_007058061.1 | n.130+227A>G | intron_variant, non_coding_transcript_variant | |||||
CC2D2A | NM_001080522.2 | c.3594+8T>C | splice_region_variant, intron_variant | NP_001073991.2 | ||||
CC2D2A | NM_001378617.1 | c.3447+8T>C | splice_region_variant, intron_variant | NP_001365546.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CC2D2A | ENST00000424120.6 | c.3594+8T>C | splice_region_variant, intron_variant | 5 | NM_001378615.1 | ENSP00000403465 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000423 AC: 6AN: 1419926Hom.: 0 Cov.: 23 AF XY: 0.00000849 AC XY: 6AN XY: 706358
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at