rs746565111
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000088.4(COL1A1):āc.4248G>Cā(p.Thr1416=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T1416T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000088.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.4248G>C | p.Thr1416= | splice_region_variant, synonymous_variant | 50/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.4050G>C | p.Thr1350= | splice_region_variant, synonymous_variant | 47/48 | ||
COL1A1 | XM_005257058.5 | c.3978G>C | p.Thr1326= | splice_region_variant, synonymous_variant | 48/49 | ||
COL1A1 | XM_005257059.5 | c.3330G>C | p.Thr1110= | splice_region_variant, synonymous_variant | 37/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.4248G>C | p.Thr1416= | splice_region_variant, synonymous_variant | 50/51 | 1 | NM_000088.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250352Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135488
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461178Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 726900
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at