rs1057524173
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000093.5(COL5A1):c.3960C>T(p.Ala1320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,551,560 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1320A) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 synonymous
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 |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.3960C>T | p.Ala1320= | synonymous_variant | 50/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.3960C>T | p.Ala1320= | synonymous_variant | 50/66 | ||
COL5A1 | XM_017014266.3 | c.3960C>T | p.Ala1320= | synonymous_variant | 50/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.3960C>T | p.Ala1320= | synonymous_variant | 50/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.3960C>T | p.Ala1320= | synonymous_variant | 50/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156780Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82532
GnomAD4 exome AF: 0.0000279 AC: 39AN: 1399400Hom.: 0 Cov.: 31 AF XY: 0.0000319 AC XY: 22AN XY: 690266
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 16, 2020 | - - |
Ehlers-Danlos syndrome, classic type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 09, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at