chr9-134824793-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BP6BS2
The NM_000093.5(COL5A1):c.4892C>A(p.Thr1631Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.4892C>A | p.Thr1631Lys | missense_variant | Exon 62 of 66 | ENST00000371817.8 | NP_000084.3 | |
COL5A1 | NM_001278074.1 | c.4892C>A | p.Thr1631Lys | missense_variant | Exon 62 of 66 | NP_001265003.1 | ||
COL5A1 | XM_017014266.3 | c.4892C>A | p.Thr1631Lys | missense_variant | Exon 62 of 65 | XP_016869755.1 | ||
LOC101448202 | NR_103451.2 | n.71-4584G>T | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.4892C>A | p.Thr1631Lys | missense_variant | Exon 62 of 66 | 1 | NM_000093.5 | ENSP00000360882.3 | ||
COL5A1 | ENST00000371820.4 | c.4892C>A | p.Thr1631Lys | missense_variant | Exon 62 of 66 | 2 | ENSP00000360885.4 | |||
COL5A1 | ENST00000460264.5 | n.360C>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 3 | |||||
COL5A1 | ENST00000465877.1 | n.72C>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249578Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135222
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727180
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:1
Has not been previously published as pathogenic or benign to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not located in the triple helical region, where the majority of pathogenic missense variants occur (Symoens et al., 2012; Stenson et al., 2014) -
Ehlers-Danlos syndrome, classic type, 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at