chr9-134823454-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000093.5(COL5A1):āc.4683A>Gā(p.Gly1561=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,856 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. G1561G) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.4683A>G | p.Gly1561= | synonymous_variant | 61/66 | ENST00000371817.8 | |
LOC101448202 | NR_103451.2 | n.71-3245T>C | intron_variant, non_coding_transcript_variant | ||||
COL5A1 | NM_001278074.1 | c.4683A>G | p.Gly1561= | synonymous_variant | 61/66 | ||
COL5A1 | XM_017014266.3 | c.4683A>G | p.Gly1561= | synonymous_variant | 61/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.4683A>G | p.Gly1561= | synonymous_variant | 61/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.4683A>G | p.Gly1561= | synonymous_variant | 61/66 | 2 | A2 | ||
COL5A1 | ENST00000460264.5 | n.151A>G | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727232
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at