2-237368929-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_004369.4(COL6A3):c.4534T>A(p.Ser1512Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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. S1512F) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.4534T>A | p.Ser1512Thr | missense_variant | 10/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.3916T>A | p.Ser1306Thr | missense_variant | 9/43 | ||
COL6A3 | NM_057166.5 | c.2713T>A | p.Ser905Thr | missense_variant | 7/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.4534T>A | p.Ser1512Thr | missense_variant | 10/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.2713T>A | p.Ser905Thr | missense_variant | 7/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.3916T>A | p.Ser1306Thr | missense_variant | 9/43 | 5 | |||
COL6A3 | ENST00000684597.1 | c.117-253T>A | intron_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at