chr12-4276004-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_001759.4(CCND2):c.196-1G>A variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001759.4 splice_acceptor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCND2 | NM_001759.4 | c.196-1G>A | splice_acceptor_variant, intron_variant | ENST00000261254.8 | NP_001750.1 | |||
CCND2-AS1 | NR_125790.1 | n.126+55C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCND2 | ENST00000261254.8 | c.196-1G>A | splice_acceptor_variant, intron_variant | 1 | NM_001759.4 | ENSP00000261254.3 | ||||
ENSG00000285901 | ENST00000674624.1 | n.196-1G>A | splice_acceptor_variant, intron_variant | ENSP00000501898.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1410986Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 701286
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | MVZ Medizinische Genetik Mainz | Sep 01, 2022 | ACMG Criteria: PVS1_STR,PM2_SUP - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.