19-9960551-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015719.4(COL5A3):āc.5098A>Gā(p.Lys1700Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015719.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A3 | NM_015719.4 | c.5098A>G | p.Lys1700Glu | missense_variant | Exon 67 of 67 | ENST00000264828.4 | NP_056534.2 | |
COL5A3 | XM_011528042.3 | c.5095A>G | p.Lys1699Glu | missense_variant | Exon 67 of 67 | XP_011526344.1 | ||
COL5A3 | XM_017026849.2 | c.2761A>G | p.Lys921Glu | missense_variant | Exon 40 of 40 | XP_016882338.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251214Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135822
GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461882Hom.: 0 Cov.: 41 AF XY: 0.0000399 AC XY: 29AN XY: 727244
GnomAD4 genome AF: 0.000236 AC: 36AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5098A>G (p.K1700E) alteration is located in exon 67 (coding exon 67) of the COL5A3 gene. This alteration results from a A to G substitution at nucleotide position 5098, causing the lysine (K) at amino acid position 1700 to be replaced by a glutamic acid (E). 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