2-188995684-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000090.4(COL3A1):c.1510-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000717 in 1,394,970 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000090.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.1510-8C>T | splice_region_variant, intron_variant | Intron 21 of 50 | ENST00000304636.9 | NP_000081.2 | ||
MIR3606 | NR_037401.1 | n.55C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
MIR3606 | unassigned_transcript_524 | n.14C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
MIR3606 | unassigned_transcript_523 | n.*19C>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.1510-8C>T | splice_region_variant, intron_variant | Intron 21 of 50 | 1 | NM_000090.4 | ENSP00000304408.4 | |||
COL3A1 | ENST00000450867.2 | c.1411-8C>T | splice_region_variant, intron_variant | Intron 20 of 49 | 1 | ENSP00000415346.2 | ||||
MIR3606 | ENST00000637672.1 | n.55C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 7.17e-7 AC: 1AN: 1394970Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 688400
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.