rs139189200
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_000393.5(COL5A2):c.2011C>T(p.Pro671Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000748 in 1,613,340 control chromosomes in the GnomAD database, including 7 homozygotes. 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. P671P) has been classified as Likely benign.
Frequency
Consequence
NM_000393.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.2011C>T | p.Pro671Ser | missense_variant | 30/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.1873C>T | p.Pro625Ser | missense_variant | 33/57 | ||
COL5A2 | XM_047443251.1 | c.1873C>T | p.Pro625Ser | missense_variant | 35/59 | ||
COL5A2 | XM_047443252.1 | c.1873C>T | p.Pro625Ser | missense_variant | 34/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.2011C>T | p.Pro671Ser | missense_variant | 30/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.850C>T | p.Pro284Ser | missense_variant | 23/47 | 5 | |||
COL5A2 | ENST00000470524.2 | n.117C>T | non_coding_transcript_exon_variant | 3/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00126 AC: 191AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00156 AC: 391AN: 251178Hom.: 3 AF XY: 0.00159 AC XY: 216AN XY: 135736
GnomAD4 exome AF: 0.000695 AC: 1015AN: 1461166Hom.: 7 Cov.: 30 AF XY: 0.000638 AC XY: 464AN XY: 726920
GnomAD4 genome ? AF: 0.00126 AC: 191AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00188 AC XY: 140AN XY: 74378
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 2 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 22, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 03, 2023 | - - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, no assertion criteria provided | clinical testing | Blueprint Genetics | Sep 17, 2014 | - - |
Ehlers-Danlos syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 19, 2020 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2019 | - - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at