chr9-134642221-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_000093.5(COL5A1):c.34G>T(p.Ala12Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000231 in 1,300,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A12T) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.34G>T | p.Ala12Ser | missense_variant | 1/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.34G>T | p.Ala12Ser | missense_variant | 1/66 | ||
COL5A1 | XM_017014266.3 | c.34G>T | p.Ala12Ser | missense_variant | 1/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.34G>T | p.Ala12Ser | missense_variant | 1/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.34G>T | p.Ala12Ser | missense_variant | 1/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000665 AC: 1AN: 150394Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000177 AC: 1AN: 56534Hom.: 0 AF XY: 0.0000298 AC XY: 1AN XY: 33558
GnomAD4 exome AF: 0.00000174 AC: 2AN: 1150216Hom.: 0 Cov.: 31 AF XY: 0.00000179 AC XY: 1AN XY: 558814
GnomAD4 genome ? AF: 0.00000665 AC: 1AN: 150394Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73392
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at