rs878853653
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000093.5(COL5A1):c.4467G>A(p.Gly1489=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G1489G) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.4467G>A | p.Gly1489= | synonymous_variant | 58/66 | ENST00000371817.8 | |
LOC101448202 | NR_103451.2 | n.144C>T | non_coding_transcript_exon_variant | 2/2 | |||
COL5A1 | NM_001278074.1 | c.4467G>A | p.Gly1489= | synonymous_variant | 58/66 | ||
COL5A1 | XM_017014266.3 | c.4467G>A | p.Gly1489= | synonymous_variant | 58/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.4467G>A | p.Gly1489= | synonymous_variant | 58/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.4467G>A | p.Gly1489= | synonymous_variant | 58/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251366Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461616Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727126
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at