rs147936946
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 7P and 2B. PM1PM2PM5PP2BP6_Moderate
The NM_000088.4(COL1A1):c.4018G>T(p.Gly1340Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,024 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1340S) has been classified as Benign.
Frequency
Consequence
NM_000088.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.4018G>T | p.Gly1340Cys | missense_variant | 50/51 | ENST00000225964.10 | NP_000079.2 | |
COL1A1 | XM_011524341.2 | c.3820G>T | p.Gly1274Cys | missense_variant | 47/48 | XP_011522643.1 | ||
COL1A1 | XM_005257058.5 | c.3748G>T | p.Gly1250Cys | missense_variant | 48/49 | XP_005257115.2 | ||
COL1A1 | XM_005257059.5 | c.3100G>T | p.Gly1034Cys | missense_variant | 37/38 | XP_005257116.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.4018G>T | p.Gly1340Cys | missense_variant | 50/51 | 1 | NM_000088.4 | ENSP00000225964.6 | ||
COL1A1 | ENST00000510710.3 | n.983G>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 36
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74268
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at