rs62184175
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The ENST00000374866.9(COL5A2):c.3689C>T(p.Thr1230Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1230R) has been classified as Likely benign.
Frequency
Consequence
ENST00000374866.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.3689C>T | p.Thr1230Ile | missense_variant | 51/54 | ENST00000374866.9 | NP_000384.2 | |
COL5A2 | XM_011510573.4 | c.3551C>T | p.Thr1184Ile | missense_variant | 54/57 | XP_011508875.1 | ||
COL5A2 | XM_047443251.1 | c.3551C>T | p.Thr1184Ile | missense_variant | 56/59 | XP_047299207.1 | ||
COL5A2 | XM_047443252.1 | c.3551C>T | p.Thr1184Ile | missense_variant | 55/58 | XP_047299208.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.3689C>T | p.Thr1230Ile | missense_variant | 51/54 | 1 | NM_000393.5 | ENSP00000364000 | P1 | |
COL5A2 | ENST00000618828.1 | c.2528C>T | p.Thr843Ile | missense_variant | 44/47 | 5 | ENSP00000482184 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250610Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135574
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727182
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2024 | The p.T1230I variant (also known as c.3689C>T), located in coding exon 51 of the COL5A2 gene, results from a C to T substitution at nucleotide position 3689. The threonine at codon 1230 is replaced by isoleucine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at