rs376920171
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_000093.5(COL5A1):c.2038C>A(p.Pro680Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,346 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P680S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.2038C>A | p.Pro680Thr | missense_variant | 21/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.2038C>A | p.Pro680Thr | missense_variant | 21/66 | ||
COL5A1 | XM_017014266.3 | c.2038C>A | p.Pro680Thr | missense_variant | 21/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.2038C>A | p.Pro680Thr | missense_variant | 21/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.2038C>A | p.Pro680Thr | missense_variant | 21/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251044Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135730
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461136Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 726912
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at