rs746339285
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_000393.5(COL5A2):āc.1814T>Cā(p.Ile605Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,614,016 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I605V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000393.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.1814T>C | p.Ile605Thr | missense_variant | 27/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.1676T>C | p.Ile559Thr | missense_variant | 30/57 | ||
COL5A2 | XM_047443251.1 | c.1676T>C | p.Ile559Thr | missense_variant | 32/59 | ||
COL5A2 | XM_047443252.1 | c.1676T>C | p.Ile559Thr | missense_variant | 31/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.1814T>C | p.Ile605Thr | missense_variant | 27/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.653T>C | p.Ile218Thr | missense_variant | 20/47 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251160Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135750
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727216
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2022 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at