rs370806359
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004369.4(COL6A3):c.5690C>T(p.Pro1897Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000663 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1897S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.5690C>T | p.Pro1897Leu | missense_variant | 12/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5072C>T | p.Pro1691Leu | missense_variant | 11/43 | ||
COL6A3 | NM_057166.5 | c.3869C>T | p.Pro1290Leu | missense_variant | 9/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.5690C>T | p.Pro1897Leu | missense_variant | 12/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.3869C>T | p.Pro1290Leu | missense_variant | 9/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5072C>T | p.Pro1691Leu | missense_variant | 11/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251446Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135918
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000688 AC XY: 50AN XY: 727242
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | COL6A3: PM2, BP4 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 27, 2021 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2021 | The c.5690C>T (p.P1897L) alteration is located in exon 12 (coding exon 11) of the COL6A3 gene. This alteration results from a C to T substitution at nucleotide position 5690, causing the proline (P) at amino acid position 1897 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at