19-9966334-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015719.4(COL5A3):āc.4762C>Gā(p.Pro1588Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000498 in 1,606,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015719.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A3 | NM_015719.4 | c.4762C>G | p.Pro1588Ala | missense_variant | Exon 64 of 67 | ENST00000264828.4 | NP_056534.2 | |
COL5A3 | XM_011528042.3 | c.4759C>G | p.Pro1587Ala | missense_variant | Exon 64 of 67 | XP_011526344.1 | ||
COL5A3 | XM_017026849.2 | c.2425C>G | p.Pro809Ala | missense_variant | Exon 37 of 40 | XP_016882338.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000819 AC: 2AN: 244112Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131718
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1454818Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 723046
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4762C>G (p.P1588A) alteration is located in exon 64 (coding exon 64) of the COL5A3 gene. This alteration results from a C to G substitution at nucleotide position 4762, causing the proline (P) at amino acid position 1588 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at