rs140851866
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_000393.5(COL5A2):c.3728G>A(p.Ser1243Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000175 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.3728G>A | p.Ser1243Asn | missense_variant | 51/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.3590G>A | p.Ser1197Asn | missense_variant | 54/57 | ||
COL5A2 | XM_047443251.1 | c.3590G>A | p.Ser1197Asn | missense_variant | 56/59 | ||
COL5A2 | XM_047443252.1 | c.3590G>A | p.Ser1197Asn | missense_variant | 55/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.3728G>A | p.Ser1243Asn | missense_variant | 51/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.2567G>A | p.Ser856Asn | missense_variant | 44/47 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000271 AC: 68AN: 251232Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135798
GnomAD4 exome AF: 0.000178 AC: 260AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.000179 AC XY: 130AN XY: 727212
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74318
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2018 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 15, 2020 | - - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at