rs139189200
Positions:
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 (★★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00069 ( 7 hom. )
Consequence
COL5A2
NM_000393.5 missense
NM_000393.5 missense
Scores
1
8
9
Clinical Significance
Conservation
PhyloP100: 4.28
Genes affected
COL5A2 (HGNC:2210): (collagen type V alpha 2 chain) This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), COL5A2. . Gene score misZ 2.4395 (greater than the threshold 3.09). Trascript score misZ 3.3523 (greater than threshold 3.09). GenCC has associacion of gene with Ehlers-Danlos syndrome, classic type, 2, Ehlers-Danlos syndrome, classic type.
BP4
Computational evidence support a benign effect (MetaRNN=0.01839903).
BP6
Variant 2-189061582-G-A is Benign according to our data. Variant chr2-189061582-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 180303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 191 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.2011C>T | p.Pro671Ser | missense_variant | 30/54 | ENST00000374866.9 | NP_000384.2 | |
COL5A2 | XM_011510573.4 | c.1873C>T | p.Pro625Ser | missense_variant | 33/57 | XP_011508875.1 | ||
COL5A2 | XM_047443251.1 | c.1873C>T | p.Pro625Ser | missense_variant | 35/59 | XP_047299207.1 | ||
COL5A2 | XM_047443252.1 | c.1873C>T | p.Pro625Ser | missense_variant | 34/58 | XP_047299208.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.2011C>T | p.Pro671Ser | missense_variant | 30/54 | 1 | NM_000393.5 | ENSP00000364000.3 | ||
COL5A2 | ENST00000618828.1 | c.850C>T | p.Pro284Ser | missense_variant | 23/47 | 5 | ENSP00000482184.1 | |||
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
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GnomAD3 exomes AF: 0.00156 AC: 391AN: 251178Hom.: 3 AF XY: 0.00159 AC XY: 216AN XY: 135736
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GnomAD4 exome AF: 0.000695 AC: 1015AN: 1461166Hom.: 7 Cov.: 30 AF XY: 0.000638 AC XY: 464AN XY: 726920
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GnomAD4 genome AF: 0.00126 AC: 191AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00188 AC XY: 140AN XY: 74378
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:2
Likely benign, no assertion criteria provided | clinical testing | Blueprint Genetics | Sep 17, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 10, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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 | - - |
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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 03, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.
REVEL
Uncertain
Sift
Benign
T;.;.
Sift4G
Benign
T;T;.
Polyphen
P;.;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at