rs778733293
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM1PP2BP4BP6BS2
The NM_000088.4(COL1A1):c.1062A>T(p.Glu354Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000088.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.1062A>T | p.Glu354Asp | missense_variant | 17/51 | ENST00000225964.10 | |
COL1A1 | XM_005257058.5 | c.1062A>T | p.Glu354Asp | missense_variant | 17/49 | ||
COL1A1 | XM_005257059.5 | c.957+654A>T | intron_variant | ||||
COL1A1 | XM_011524341.2 | c.958-182A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.1062A>T | p.Glu354Asp | missense_variant | 17/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000471344.1 | n.6A>T | non_coding_transcript_exon_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151528Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250056Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135390
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461664Hom.: 0 Cov.: 35 AF XY: 0.00000825 AC XY: 6AN XY: 727148
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151528Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73970
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Sep 29, 2020 | - - |
Connective tissue disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Jun 01, 2018 | - - |
Osteogenesis imperfecta type I Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at