NM_015719.4:c.4657C>T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015719.4(COL5A3):c.4657C>T(p.His1553Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,543,728 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 Uncertain significance (★).
Frequency
Consequence
NM_015719.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A3 | NM_015719.4 | c.4657C>T | p.His1553Tyr | missense_variant | Exon 63 of 67 | ENST00000264828.4 | NP_056534.2 | |
COL5A3 | XM_011528042.3 | c.4654C>T | p.His1552Tyr | missense_variant | Exon 63 of 67 | XP_011526344.1 | ||
COL5A3 | XM_017026849.2 | c.2320C>T | p.His774Tyr | missense_variant | Exon 36 of 40 | XP_016882338.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000140 AC: 2AN: 142412Hom.: 0 AF XY: 0.0000257 AC XY: 2AN XY: 77918
GnomAD4 exome AF: 0.00000647 AC: 9AN: 1391502Hom.: 0 Cov.: 35 AF XY: 0.00000583 AC XY: 4AN XY: 686460
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4657C>T (p.H1553Y) alteration is located in exon 63 (coding exon 63) of the COL5A3 gene. This alteration results from a C to T substitution at nucleotide position 4657, causing the histidine (H) at amino acid position 1553 to be replaced by a tyrosine (Y). 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