2-237357826-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004369.4(COL6A3):c.6528C>A(p.Leu2176=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L2176L) has been classified as Likely benign.
Frequency
Consequence
NM_004369.4 synonymous
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 |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.6528C>A | p.Leu2176= | synonymous_variant | 22/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5910C>A | p.Leu1970= | synonymous_variant | 21/43 | ||
COL6A3 | NM_057166.5 | c.4707C>A | p.Leu1569= | synonymous_variant | 19/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.6528C>A | p.Leu2176= | synonymous_variant | 22/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.4707C>A | p.Leu1569= | synonymous_variant | 19/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5910C>A | p.Leu1970= | synonymous_variant | 21/43 | 5 | |||
COL6A3 | ENST00000493475.2 | n.58C>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251478Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135914
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461780Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727196
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at