chr4-108832435-TA-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_198721.4(COL25A1):c.1657-3del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000958 in 1,586,440 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198721.4 splice_region, splice_polypyrimidine_tract, 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 | UniProt |
---|---|---|---|---|---|---|---|
COL25A1 | NM_198721.4 | c.1657-3del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000399132.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL25A1 | ENST00000399132.6 | c.1657-3del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_198721.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151742Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000105 AC: 150AN: 1434698Hom.: 0 Cov.: 26 AF XY: 0.0000952 AC XY: 68AN XY: 714434
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151742Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74098
ClinVar
Submissions by phenotype
COL25A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at