chr17-50188120-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000088.4(COL1A1):c.3237C>T(p.Gly1079=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,580,858 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. G1079G) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.3237C>T | p.Gly1079= | synonymous_variant | 44/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.3039C>T | p.Gly1013= | synonymous_variant | 41/48 | ||
COL1A1 | XM_005257058.5 | c.2967C>T | p.Gly989= | synonymous_variant | 42/49 | ||
COL1A1 | XM_005257059.5 | c.2319C>T | p.Gly773= | synonymous_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.3237C>T | p.Gly1079= | synonymous_variant | 44/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000486572.1 | n.435C>T | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
COL1A1 | ENST00000511732.1 | n.561C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000208 AC: 4AN: 192494Hom.: 0 AF XY: 0.00000962 AC XY: 1AN XY: 103992
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1428704Hom.: 0 Cov.: 36 AF XY: 0.0000141 AC XY: 10AN XY: 708106
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at