rs755289850
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_000093.5(COL5A1):c.1114G>A(p.Ala372Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A372D) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.1114G>A | p.Ala372Thr | missense_variant | 7/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.1114G>A | p.Ala372Thr | missense_variant | 7/66 | ||
COL5A1 | XM_017014266.3 | c.1114G>A | p.Ala372Thr | missense_variant | 7/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.1114G>A | p.Ala372Thr | missense_variant | 7/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.1114G>A | p.Ala372Thr | missense_variant | 7/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152226Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250946Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135754
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461748Hom.: 0 Cov.: 35 AF XY: 0.0000248 AC XY: 18AN XY: 727200
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152226Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at