9-134820184-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000093.5(COL5A1):c.4515C>T(p.Leu1505Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L1505L) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.4515C>T | p.Leu1505Leu | synonymous_variant | Exon 58 of 66 | ENST00000371817.8 | NP_000084.3 | |
COL5A1 | NM_001278074.1 | c.4515C>T | p.Leu1505Leu | synonymous_variant | Exon 58 of 66 | NP_001265003.1 | ||
COL5A1 | XM_017014266.3 | c.4515C>T | p.Leu1505Leu | synonymous_variant | Exon 58 of 65 | XP_016869755.1 | ||
LOC101448202 | NR_103451.2 | n.96G>A | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.4515C>T | p.Leu1505Leu | synonymous_variant | Exon 58 of 66 | 1 | NM_000093.5 | ENSP00000360882.3 | ||
COL5A1 | ENST00000371820.4 | c.4515C>T | p.Leu1505Leu | synonymous_variant | Exon 58 of 66 | 2 | ENSP00000360885.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251312Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135878
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461608Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727112
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
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Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at