rs201256042
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000088.4(COL1A1):c.4017C>T(p.Gly1339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,613,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G1339G) has been classified as Likely benign.
Frequency
Consequence
NM_000088.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.4017C>T | p.Gly1339= | synonymous_variant | 50/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.3819C>T | p.Gly1273= | synonymous_variant | 47/48 | ||
COL1A1 | XM_005257058.5 | c.3747C>T | p.Gly1249= | synonymous_variant | 48/49 | ||
COL1A1 | XM_005257059.5 | c.3099C>T | p.Gly1033= | synonymous_variant | 37/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.4017C>T | p.Gly1339= | synonymous_variant | 50/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000510710.3 | n.982C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248724Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134820
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460920Hom.: 0 Cov.: 36 AF XY: 0.0000537 AC XY: 39AN XY: 726750
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 02, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at