rs199755089
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000093.5(COL5A1):c.1191G>A(p.Ala397=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,222 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. A397A) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.1191G>A | p.Ala397= | synonymous_variant | 8/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.1191G>A | p.Ala397= | synonymous_variant | 8/66 | ||
COL5A1 | XM_017014266.3 | c.1191G>A | p.Ala397= | synonymous_variant | 8/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.1191G>A | p.Ala397= | synonymous_variant | 8/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.1191G>A | p.Ala397= | synonymous_variant | 8/66 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248916Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134762
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152352Hom.: 0 Cov.: 34 AF XY: 0.0000268 AC XY: 2AN XY: 74498
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at