chr17-50192029-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000088.4(COL1A1):c.1984-5C>G 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 0.00000806 in 1,611,936 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_000088.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.1984-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000225964.10 | |||
COL1A1 | XM_005257058.5 | c.1984-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
COL1A1 | XM_005257059.5 | c.1066-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
COL1A1 | XM_011524341.2 | c.1786-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.1984-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000088.4 | P1 | |||
COL1A1 | ENST00000504289.1 | n.411C>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
COL1A1 | ENST00000476387.1 | n.333-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244168Hom.: 0 AF XY: 0.0000227 AC XY: 3AN XY: 132230
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459790Hom.: 0 Cov.: 44 AF XY: 0.0000138 AC XY: 10AN XY: 725904
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at